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Variant detection in next-generation sequencing data
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From: Iva O. <Iva...@lf...> - 2023-09-27 10:59:30
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Dear all, I am new to VarScan and I would like to ask a question that I can't find an answer to on the forums. What do the numerical values for somatic status mean? If I understand that correctly, 1 indicates a germline variant, 2 indicates a somatic variant and 3 indicates an LOH event. But what do values 0 and 5 stand for? Thank you very much. Best regards, Iva Ondečková, MD |
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From: Baiba A. <bai...@gm...> - 2020-09-17 11:50:50
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Hello, I try to perform Varscan together with mpileup, however there is empty output are there some common problems? -- Ar cieņu, Baiba Alkšere |
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From: Baiba A. <bai...@gm...> - 2020-09-07 05:06:29
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Hello, I would like to use VarScan for SARS-COV-2 variant calling from bam files. I am confused, if I can use merged (samtools merge -c -f ) option, to get input files. Also, if only piled -up inputs are needed - which would be the correct pile up command for RNA-Seq files? I dont actually get, which command use for RNA-Seq files - can I use somatic mutation pipeline? I see, that normal pileup file is required for input in that case. But I dont have any normal seq files from coronavirus NGS.. Thank You! -- Ar cieņu, Baiba Alkšere |
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From: Wright, A. <ali...@uc...> - 2016-11-02 12:21:40
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I would be very grateful if you could explain why --min-freq-for-hom is not 1-min-var-freq. Instead the recommended parameters are -min-var-freq 0.2 and -min-freq-for-hom 0.75 (Koboldt et al 2013). Is there a reason to define different parameters? Thanks Alison --- Dr Alison Wright Postdoctoral Research Associate University College London Department of Genetics, Evolution and Environment The Darwin Building Gower Street London WC1E 6BT www.alisonewright.co.uk<http://www.alisonewright.co.uk> |
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From: Noa H. <he...@di...> - 2016-03-28 18:01:59
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ID chrom loc.start loc.end num.mark seg.mean bstat pval lcl ucl Sample.1 1 10232313 10296666 26 53.1808 4.9181300400547 1.67866807612427e-05 10295748 10296881 Sample.1 1 10296881 10297166 4 103.35 5.60574974491425 1.49117272796527e-06 10297166 10321697 Sample.1 10 43100443 78040188 56 46.8625 8.0811826404418 3.02035778358618e-14 78037281 86755006 Sample.1 10 86755006 86755706 8 121.35 7.0321582472234 2.73361201045886e-11 86755706 86755706 Sample.1 10 86755806 86756985 9 23.8667 9.53129906526965 1.40643848751213e-20 86756985 86756985 Sample.1 10 86838856 86843497 4 105 5.93377234391684 1.25367143290413e-07 86843497 86890051 Sample.1 12 12717823 68836749 42 61.5738 4.75022809252694 5.17624018765918e-05 68835818 68839388 Sample.1 12 68839258 68839588 5 123.12 7.63184432628579 1.78053731434406e-12 68839388 68839688 Sample.1 13 32316445 32331027 14 38.45 8.07923174073822 1.30338803010092e-14 32330911 32332256 Sample.1 13 32332256 32333154 10 134.75 11.2900419369405 1.63211832394939e-27 32333054 32333254 Sample.1 14 24239781 75042414 129 53.0054 5.22823300891012 8.86888946578543e-06 75032052 75046665 Sample.1 14 75046365 75048143 20 82.47 4.44234993231548 0.000273265473844257 75047443 75049207 Sample.1 14 75048250 95107864 53 60.6321 5.95378120811237 9.95748569177357e-08 95107592 95111401 Sample.1 14 95107964 95115751 12 99.5583 8.14080046694529 2.02798036528707e-14 95113076 95116437 Sample.1 16 2048600 3583497 90 37.5711 4.09421996872615 0.00139038672785948 2088020 3588986 Sample.1 16 3584753 3589786 11 58.7636 5.00691649352091 9.31337576739452e-06 3589786 3590286 Sample.1 16 3589886 3591133 14 99.1571 5.84971592253212 3.2699414022027e-07 3590833 3595599 Sample.1 16 3591233 89758661 181 58.2563 4.00616852887034 0.00277403219084203 68801856 89778926 Sample.1 17 7669600 7687366 28 65.5429 15.5959283495723 2.32900068496366e-53 7687366 7687366 Sample.1 17 7687596 7688096 6 197.2833 13.945483340984 5.85673333490087e-42 7688096 7688096 Sample.1 17 7688196 43091419 248 52.529 5.75764585152282 6.7758075260985e-07 43045662 43093361 Sample.1 17 43091519 58734202 73 72.1765 4.61854023120482 0.00019667144343092 48728077 61683608 Sample.1 19 1206905 10991244 39 35.2205 4.05136341576925 0.00126906751749501 10986577 11010465 Sample.1 19 10994812 11023512 20 56.645 5.91103432541324 1.8015683948379e-07 11010465 11027769 Sample.1 2 3575594 29532099 67 50.6015 3.82948729575959 0.00340091235640808 29275493 29532099 Sample.1 2 29694834 29920186 8 15.5 3.77099986668074 0.00137839362167691 29919986 29920412 Sample.1 2 29920286 37893567 6 5.9167 3.86616143328356 0.00312272706630348 29920561 47373892 Sample.1 2 37893667 47798695 78 26.3667 4.76492185910509 6.83825724663061e-05 47790915 47798995 Sample.1 2 47798795 47799538 9 48.1444 4.898040458714 2.23938585557193e-05 47799238 47800064 Sample.1 2 47799638 47806873 30 29.03 4.85899236403179 5.30589467457243e-05 47806636 58241202 Sample.1 5 224344 1254422 20 30.9 4.78484384459633 4.72542477071763e-05 1253812 1271211 Sample.1 5 1255271 1294187 33 66.403 4.23355475912591 0.000558903611107522 1279375 1294386 Sample.1 5 1294286 112737014 19 33.8158 10.7136983692152 1.57451902381462e-25 112737014 112737014 Sample.1 5 112737114 112737314 3 173.3667 11.2330688478066 6.39641934735134e-28 112737314 112737314 Sample.1 5 112737355 112818950 24 43.7042 4.04220907921668 0.00224052820527075 112792530 112838305 Sample.1 5 112819050 138925340 173 62.7942 6.48191039892513 6.85250043143824e-09 138904333 138930457 Sample.1 7 5977674 117504247 185 52.6503 3.71075793350722 0.00805104679348054 116755444 117534260 Sample.1 7 117504347 117590344 29 35.6172 4.31623551011501 0.00035075104458192 117559436 117592120 Sample.1 7 117591920 117603614 14 58.3857 5.77943899228187 2.95518722001616e-07 117602719 117606759 Sample.1 7 117603676 148816783 58 34.9534 8.47813310607157 1.18688179605518e-15 148815490 148817206 Sample.1 7 148817206 148828824 14 71.2 5.91022818629352 6.0951317684572e-08 148828724 148829712 Sample.1 7 148829712 152648729 10 36.65 3.23169710097314 0.0121107293862329 152648629 152649268 Sample.1 Y 2786741 6874088 23 20.0696 5.22630883073514 4.35995531164312e-06 6873979 13757676 Sample.1 Y 8740864 19735519 18 37.0111 3.96316431793479 0.00152896139921172 13757814 20579670 |
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From: Noa H. <he...@di...> - 2016-03-18 17:29:12
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I didn’t mention before that the output table is truncated, although the data that is written until that point makes sense. From: henig Date: Friday, March 18, 2016 at 1:19 PM To: "var...@li...<mailto:var...@li...>" Subject: Exception from varscan copynumber Hi, I am using varscan for variant calling and recently tried running varscan 2.3.7 for copy number variation. I received the following exception, which was reported by other users before, but I’m not sure if I should just ignore it and use the output. This is command I ran: java -jar varscan-2.3.7.jar copynumber AE.normal.pileup KP.tumor.pileup --data-ratio 0.68 And this is the output (in addition to the table): Normal Pileup: AE.normal.pileup Tumor Pileup: KP.tumor.pileup Min coverage:10 Min avg qual:15 P-value thresh:0.01 Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 5 at net.sf.varscan.Copynumber.<init>(Copynumber.java:693) at net.sf.varscan.VarScan.copynumber(VarScan.java:317) at net.sf.varscan.VarScan.main(VarScan.java:198) I downloaded the most recent jar 2.3.9 and still getting a similar error: Normal Pileup: ../AE.normal.pileup Tumor Pileup: ../KP.tumor.pileup Min coverage:10 Min avg qual:15 P-value thresh:0.01 Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 5 at net.sf.varscan.Copynumber.<init>(Copynumber.java:693) at net.sf.varscan.VarScan.copynumber(VarScan.java:328) at net.sf.varscan.VarScan.main(VarScan.java:209) I am mostly curious to know if this exception affects in any way the output that is generated? Thank you, Noa Henig |
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From: Noa H. <he...@di...> - 2016-03-18 16:53:01
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Hi, I am using varscan for variant calling and recently tried running varscan 2.3.7 for copy number variation. I received the following exception, which was reported by other users before, but I’m not sure if I should just ignore it and use the output. This is command I ran: java -jar varscan-2.3.7.jar copynumber AE.normal.pileup KP.tumor.pileup --data-ratio 0.68 And this is the output (in addition to the table): Normal Pileup: AE.normal.pileup Tumor Pileup: KP.tumor.pileup Min coverage: 10 Min avg qual: 15 P-value thresh: 0.01 Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 5 at net.sf.varscan.Copynumber.<init>(Copynumber.java:693) at net.sf.varscan.VarScan.copynumber(VarScan.java:317) at net.sf.varscan.VarScan.main(VarScan.java:198) I downloaded the most recent jar 2.3.9 and still getting a similar error: Normal Pileup: ../AE.normal.pileup Tumor Pileup: ../KP.tumor.pileup Min coverage: 10 Min avg qual: 15 P-value thresh: 0.01 Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 5 at net.sf.varscan.Copynumber.<init>(Copynumber.java:693) at net.sf.varscan.VarScan.copynumber(VarScan.java:328) at net.sf.varscan.VarScan.main(VarScan.java:209) I am mostly curious to know if this exception affects in any way the output that is generated? Thank you, Noa Henig |
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From: Kevin B. <kev...@gm...> - 2016-03-16 02:58:49
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I noticed that at http://dkoboldt.github.io/varscan/ in the Installing VarScan section. there's a link to the User's Manual in this sentence: Usage information will be displayed. For details on using VarScan, please see the User's Manual. that points to http://dkoboldt.github.io/varscan/doc/index.html which appears to be the JavaDoc class reference extraction and not the User's Manual. that is linked to from the side-bar, vis: http://dkoboldt.github.io/varscan/using-varscan.html And the reason I came across this was that I'd made a note, when coming to install VarScan for someone in our School of Biological Sciences, that it had a depency on bam-readcount, but couldn;'t recall where I'd seen that info. It appears to be in the VarScan.v2.4.0.description.txt file that's in the doanload but not, as far as I can see from the online docs, in the online docs. Hope that helps, Kevin M. Buckley eScience Consultant School of Engineering and Computer Science Victoria University of Wellington New Zealand |
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From: TUNC M. <tmo...@ku...> - 2016-02-01 10:16:57
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Dear all hi, Even though there is a —output-vcf 1 option reported for mpileupsnp mode, i couldnt find this option for somatic mutation calling mode. I would like to have my output in VCF format. Therefore I will be more than glad if you can show me a way to do this. Which option should I try? Best regards, Tunc. |
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From: Ogan A. <oab...@gm...> - 2015-10-02 15:38:31
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I am running VarScan 2.4.0 on a trio test set, and I am getting lines where the STATUS= (empty string), which kills downstream tools like bcftools with this same error here (https://github.com/samtools/bcftools/issues/303). Since status is defined as a number, it expects to have a value, I can fix it manually by making is STATUS=0, but it maybe fixed somewhere else. Any thoughts. Thank you |
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From: Stephanie De V. <st...@ps...> - 2015-01-20 15:41:51
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Dear all, when applying Varscan filter to an output file from mpileup2snp, filtering for frequency 0.25, with the following command line, java -Xmx50g -d64 -jar /software/shared/apps/x86_64/VarScan/2.3.7/VarScan.v2.3.7.jar filter miseqSNPs.txt --min-var-freq 0.25 --output-file miseqSNPs_allelfreq_over_25.txt I get the following error: Currently Loaded Modulefiles: 1) /perl/x86_64/5.14.1 7) /mpc/x86_64/0.8.1 2) /gridengine/x86_64/2011.11 8) /gcc/x86_64/4.8.0 3) /java/x86_64/1.7.0_21 9) /python/x86_64/3.4.1 4) /bwa/x86_64/0.5.9 10) /samtools/x86_64/1.1 5) /gmp/x86_64/4.3.2 11) /VarScan/x86_64/2.3.7 6) /mpfr/x86_64/2.4.2 Picked up JAVA_TOOL_OPTIONS: -XX:ParallelGCThreads=1 Min coverage: 10 Min reads2: 2 Min strands2: 1 Min var freq: 0.25 Min avg qual: 15 P-value thresh: 0.1 Reading input from miseqSNPs.txt Parsing Exception on line: scaffold_1 1279 C G G:11:0:11:100%:1.4176E-6 Pass:0:0:4:7:1E0 0 0 1 0 G:11:0:11:100%:1.4176E-6 For input string: "G:11:0:11:100%:1.4176E-6" Parsing Exception on line: scaffold_1 1397 A C C:8:0:8:100%:7.77E-5 Pass:0:0:4:4:1E0 0 0 1 0 C:8:0:8:100%:7.77E-5 For input string: "C:8:0:8:100%:7.77E-5" Parsing Exception on line: scaffold_1 1415 A C C:9:0:9:100%:2.0568E-5 Pass:0:0:4:5:1E0 0 0 1 0 C:9:0:9:100%:2.0568E-5 For input string: "C:9:0:9:100%:2.0568E-5" Parsing Exception on line: scaffold_1 1459 A G G:9:0:9:100%:2.0568E-5 Pass:0:0:5:4:1E0 0 0 1 0 G:9:0:9:100%:2.0568E-5 For input string: "G:9:0:9:100%:2.0568E-5" Parsing Exception on line: scaffold_1 2535 C T T:8:0:8:100%:7.77E-5 Pass:0:0:4:4:1E0 0 0 1 0 T:8:0:8:100%:7.77E-5 For input string: "T:8:0:8:100%:7.77E-5" Too many parsing exceptions encountered; exiting Does anyone know why these parsing exceptions occur? Kind regards, Stephanie |
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From: Stephanie De V. <st...@ps...> - 2015-01-19 14:33:12
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Dear all, I am looking for SNPs in a 24G mpileup file, based on DNA of one sample. While submitting the following commands in a shell script (qsub -l h_vmem=100G -l h_stack=700m varscan.sh) using the following command line samtools mpileup -q 1 -B -I -f assembly.fasta allmiseq_sorted_rmdup.bam > allmiseq_sorted_rmdup.mpileup java -Xmx100g -d64 -jar /software/shared/apps/x86_64/VarScan/2.3.7/VarScan.v2.3.7.jar mpileup2snp allmiseq_sorted_rmdup.mpileup miseqSNPs.txt the mpileup is produced, but no SNP file is produced. This is the Output file Mon Jan 19 11:52:26 CET 2015 cyclone2.psblocal Error occurred during initialization of VM Could not reserve enough space for object heap This is the Error file Currently Loaded Modulefiles: 1) /perl/x86_64/5.14.1 7) /mpc/x86_64/0.8.1 2) /gridengine/x86_64/2011.11 8) /gcc/x86_64/4.8.0 3) /java/x86_64/1.7.0_21 9) /python/x86_64/3.4.1 4) /bwa/x86_64/0.5.9 10) /samtools/x86_64/1.1 5) /gmp/x86_64/4.3.2 11) /VarScan/x86_64/2.3.7 6) /mpfr/x86_64/2.4.2 Picked up JAVA_TOOL_OPTIONS: -XX:ParallelGCThreads=1 Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit. Does anyone know what could cause these memory problems? I didn`t think VarScan needed that much memory. With kind regards -- Stephanie De Vos PhD in Bioscience Engineering Scientific collaborator at the Laboratory of Aquaculture & Artemia Reference Center Faculty of Bioscience Engineering - Department of Animal Production Ghent University Tel:+32 (0)9 331 38 63 http://www.aquaculture.ugent.be “The essence of open-mindedness is forcing your beliefs to conform to the evidence of observations, not forcing observations to conform to your beliefs.” Professor Lawrence Krauss, Theoretical Physicist |
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From: Julie Lee-Y. <jul...@ya...> - 2014-12-02 13:05:28
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Hello, I'm a new user of VarScan. I am working with pooled samples (pools of 25) thus my samtools mpileup file represents a "single sample" in the sense that all reads in the bam file are treated together but "multiple samples" in the sense that the output from the samtools mpileup command summarizes reads from multiple individuals. I am wanting to use VarScan to make consensus calls. Unlike the pileup2cns command, the mpileup command seems to output exactly what I want (output in vcf format and list all positions, not just variants; as well as allows from strand filtering). But I'm wondering if it is inappropriate to use this command when the mpileup is from a single bam file (it doesn't in practice throw any errors but are there any problems with using the suite of mpileup commands on a mpileup from a single bam)? Is the only difference between the commands that mpileup2cns has the ability to base calls on multiple samples or are there other important differences? Thanks in advance for the help! |
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From: Harpreet S. <Har...@as...> - 2014-09-17 09:29:49
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Hi,
I am using varScan2.3.7 and running copynumber command for normal-tumor pairs and getting the following ArrayIndexOutOfBoundsException error.
java -jar VarScan.v2.3.7.jar copynumber CS.mpileup CR.mpileup CR
Normal Pileup: CS.mpileup
Tumor Pileup: CR.mpileup
Min coverage: 10
Min avg qual: 15
P-value thresh: 0.01
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 5
at net.sf.varscan.Copynumber.<init>(Copynumber.java:693)
at net.sf.varscan.VarScan.copynumber(VarScan.java:317)
at net.sf.varscan.VarScan.main(VarScan.java:198)
Any solution how to fix this?
Thanks,
Harpreet
=============================
Dr. Harpreet Kaur Saini
Associate Director, Bioinformatics
Astex Pharmaceuticals
436 Cambridge Science Park
Cambridge CB4 0QA
United Kingdom
Phone: +44 (0) 1223 226266
This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately.
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From: VG <gup...@gm...> - 2014-08-11 15:11:55
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Hi Everyone, I started using varscan to find T ----> C mutations in my sample. I am using pileup2snp command I need to understand what does this parameter means --min-avg-qual Minimum base quality at a position to count a read [15] How is this value calculated?? Hope to hear from you soon. Regards Varun |
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From: Andrew W. <and...@gm...> - 2014-04-28 18:56:26
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Dear varscan support team,
I tried to use varscan copy number, but exceptions always occurred. Two
typical cases were provided below, from two independent pileup files and
two normal-tumor mipileup files (bam files). The samtools-0.1.19 mpileup
was used to make the pileup files. Those pileup files work for somatic
and snp call functions from varscan, but exceptions were called during
copynumber. Could you please guide to avoid them? Thanks.
1) from two independent pileup file, like java -jar varScan.v2.3.6.jar
copynumber normal.pileup tumor.pileup outputname
Min coverage: 10
Min avg qual: 15
P-value thresh: 0.01
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 5
at net.sf.varscan.Copynumber.<init>(Copynumber.java:693)
at net.sf.varscan.VarScan.copynumber(VarScan.java:317)
at net.sf.varscan.VarScan.main(VarScan.java:198)
2)from two bam file or two normal-tumor pileup files using --mpileup 1
[mpileup] 2 samples in 2 input files
<mpileup> Set max per-file depth to 4000
Min coverage: 10
Min avg qual: 15
P-value thresh: 0.01
Reading input from /dev/fd/63
Reading mpileup input...
Parsing Exception on line:
1 3010821 G 4 ..., E78F 0
Best,
Andrew
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From: NextGenSeb <nex...@gm...> - 2013-09-26 01:08:57
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Dear all, I am attempting to call a 18bp deletion which is located right after a SNP using Varscan. Unfortunately, this doesn't work. While the SNP is called using mpileup2cns or mpileup2snp, the deletion is missed by both mpileup2indel and mpileup2cns. The deletion is clearly present in the mpileup, and artificially removing the SNP in front of the deletion and replacing it with a match results in hte deletion being called successfully. The command I used: $java -jar VarScan.v2.3.6.jar mpileup2indel test.mpileup --variants --output-vcf 1 --min-var-freq 0.001 --p-value 0.01 --min-coverage 50 --min-reads2 5 --min-avg-qual 15 --strand-filter 0 > test.vcf java version "1.7.0_04" samtools Version: 0.1.19-44428cd I have posted to the mailing list with example data, but it got stuck due to file size... So here just an snippet from the mpileup: chr7 55242467 A 4228 T-18ATTAAGAGAAGCAACATC.T-18ATTAAGAGAAGCAACATC......T-18ATTAAGAGAAGCAACATCT-18ATTAAGAGAAGCAACATCT-18ATTAAGAGAAGCAACATCT-18ATTAAGAGAAGCAACATC.T-18ATTAAGAGAAGCAACATCT-18ATTAAGAGAAGCAACATCT-18ATTAAGAGAAGCAACATCT-18ATTAAGAGAAGCAACATC...T-18ATTAAGAGAAGCAACATC.T-18ATTAAGAGAAGCAACATC..T-18ATTAAGAGAAGCAACATC.T-18ATTAAGAGAAGCAACATC.T-18ATTAAGAGAAGCAACATCT-18ATTAAGAGAAGCAACATC....T-18ATTAAGAGAAGCAACATC..T-18ATTAAGAGAAGCAACATC..T-18ATTAAGAGAAGCAACATC...T-18ATTAAGAGAAGCAACATC..T-18ATTAAGAGAAGCAACATC...T-18ATTAAGAGAAGCAACATCT-18ATTAAGAGAAGCAACATCT-18ATTAAGAGAAGCAACATC......T-18ATTAAGAGAAGCAACATCT-18ATTAAGAGAAGCAACATCT-18ATTAAGAGAAGCAACATC....*. Please note, this is very deep coverage data (>2000x), hence I won't post the full entry here. But I hope it will suffice to clarify my case Any advice would be greatly apprechiated. Cheers Seb |
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From: Mehaffey, M. (NIH/N. [C] <meh...@ma...> - 2013-07-16 14:52:48
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I'm having trouble getting the copynumber function of VarScan 2.3.4 or 2.3.5 to work.
Trying to run with 2 mpileup files gives 1 error:
java -jar /usr/local/apps/varscan/2.3.5/VarScan.v2.3.5.jar copynumber normal.mpileup tumor.mpileup out.cnv
Normal Pileup: normal.mpileup
Tumor Pileup: tumor.mpileup
Min coverage: 10
Min avg qual: 15
P-value thresh: 0.01
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 5
at net.sf.varscan.Copynumber.<init>(Copynumber.java:741)
at net.sf.varscan.VarScan.copynumber(VarScan.java:301)
at net.sf.varscan.VarScan.main(VarScan.java:193)
Trying to use 1 mpileup file for the pair I get the following error:
java -jar VarScan.v2.3.5.jar copynumber Test.mplieup --mpileup 1
Min coverage: 10
Min avg qual: 15
P-value thresh: 0.01
Reading input from Test.mplieup
Reading mpileup input...
Parsing Exception on line:
chr1 13167 G 10 .,,.,,,,,, IJEJIIAHII 0
8
Any help is appreciated.
Thank you,
Michele Mehaffey
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From: Lei Xu <le...@st...> - 2012-09-13 01:31:53
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Hello I wonder if anyone else has encountered this issue yet, but I'm trying to merge several vcf files from different variant callers (incl. varscan) using vcf-merge (by vcftools). However it throws errors because the varscan vcf indel file is not formatted as expected (as detailed on the 1000genomes website). Specifically, indels, as called by other variant callers such as GATK usually follow this format : "For InDels, the reference String must include the base before the event (which must be reflected in the POS field). (String, Required)." GATK example: chr1 98373 . TC T 212.43 filter AC=2;AF=1.00;AN=2;DP=24;FS=0.000;HRun=2;HaplotypeScore=17.6155;MQ0=4;MQ=21.00;QD=8.85;SB=-0.00;SF=0f GT:GQ:DP:PL:AD . 1/1:18.06:6:254,18,0:18,6 Varscan example: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR chr1 10230 . A -C . PASS DP=2597;SOMATIC;SS=2;SSC=209;GPV=1E0;SPV=1.0584E-21 GT:GQ:DP:RD:AD:FREQ 1/1:.:886:102:10:8.93% 0/1:.:1711:434:505:53.78% I could not find a detailed explanation about the indel output on the website. Can someone help me interpret this deletion? Has anyone else encountered this issue? Thanks -Lei |
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From: Sheng Li <she...@gm...> - 2012-03-29 05:29:08
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Hi All, Does VarScan.v2.2.10.jar somaticFilter support the vcf format input? I have tried to call snp and indels using VarScan.v2.2.10.jar somatic and the output format is vcf, which looks good. However, when I tried to filter the vcf format snp file, I got the following errors. I was wondering if varscan v2.2.10 somaticFilter still only take non-vcf format? How can I filter the vcf output of varscan somatic? Thanks! $varscan somaticFilter Sample.snp --min-strands2 2 --min-avg-qual 30 --indel-file Sample.indel --output-file Sample.fltsnp Error Parsing Indel File: 1 Window size: 10 Window SNPs: 3 Indel margin: 3 Reading input from Sample.snp 16 cluster SNPs identified Reading input from Sample.snp Parsing Exception on line: ##source=VarScan2 1 Parsing Exception on line: ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases"> 1 Parsing Exception on line: ##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (Germline, LOH, Somatic, or Unknown)"> 1 Parsing Exception on line: ##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls"> 1 Parsing Exception on line: ##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls"> 1 Too many parsing exceptions encountered; exiting My vcf file from varscan somatic: ##fileformat=VCFv4.0 ##source=VarScan2 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases"> ##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (Germline, LOH, Somatic, or Unknown)"> ##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls"> ##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls"> ##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> ##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> ##FORMAT=<ID=RDS1,Number=1,Type=Integer,Description="Reference-supporting reads"> ##FORMAT=<ID=RDS2,Number=1,Type=Integer,Description="Variant-supporting reads"> ##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR chr1 139570 . C G . PASS DP=44;SS=Somatic;GPV=1E0;SPV=3.3075E-3 GT:GQ:DP:RDS1:RDS2:FREQ 0/0:.:23:21:2:8.7% 0/1:.:21:10:10:50% chr1 140177 . A C . PASS DP=121;SS=Germline;GPV=3.7001E-12;SPV=1.9829E-1 GT:GQ:DP:RDS1:RDS2:FREQ 0/1:.:52:39:12:23.53% 0/1:.:69:46:22:32.35% chr1 140369 . T C . PASS DP=142;SS=Germline;GPV=6.8521E-65;SPV=9.4524E-1 GT:GQ:DP:RDS1:RDS2:FREQ 1/1:.:56:1:46:97.87% 1/1:.:86:5:73:93.59% chr1 140410 . T A . PASS DP=123;SS=Germline;GPV=6.3633E-15;SPV=5.0628E-1 GT:GQ:DP:RDS1:RDS2:FREQ 0/1:.:50:31:16:34.04% 0/1:.:73:45:25:35.71% chr1 140473 . A G . PASS DP=66;SS=Germline;GPV=5.2337E-6;SPV=8.7967E-1 GT:GQ:DP:RDS1:RDS2:FREQ 0/1:.:28:18:8:30.77% 0/1:.:38:30:8:21.05% Cheers, Sheng |
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From: Yi, M. (NIH/N. [C] <yi...@ma...> - 2012-03-12 18:36:42
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Hi, List: I recently just start to use VarScan to run SNP calling on our exome-seq data, here is the command I used : samtools mpileup -f hg19.fa F2.bam F3.bam F4.bam F9.bam F10.bam | java -jar /opt/nasapps/stow/VarScan_v2.2.8/bin/VarScan.v2.2.8.jar mpileup2snp --output-vcf 1 --min-coverage 10 --min-avg-qual 20 --min-var-freq 0.25 --p-value 1e-06 > /VarScanResult/VarScan_mpileup.vcf and I got a vcf file with first few data rows as below (take out the header part): ....(header lines) #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 Sample2 Sample3 Sample4 Sample5 chrM 119 T C . PASS DP=101 GT:GQ:DP 0/0:2:15 0/0:4:24 0/0:4:21 0/0:3:20 1/1:11:21 chrM 146 T C . PASS DP=58 GT:GQ:DP ./.:.:9 ./.:.:6 ./.:.:9 ./.:.:10 0/0:4:24 chrM 150 T C . PASS DP=24 GT:GQ:DP ./.:.:5 ./.:.:4 ./.:.:3 ./.:.:4 ./.:.:8 chrM 152 T C . PASS DP=51 GT:GQ:DP ./.:.:8 ./.:.:8 ./.:.:5 ./.:.:8 0/0:4:22 chrM 189 A G . PASS DP=110 GT:GQ:DP 0/0:4:21 0/0:5:31 0/0:2:15 0/0:4:26 1/1:9:17 chrM 195 C T . PASS DP=56 GT:GQ:DP ./.:.:7 1/1:6:14 ./.:.:8 ./.:.:7 0/0:3:20 as you can see, the ID column seem having no content but was filled with contents from shifted column from right "REF" column. In other words, for example, the first record's ID is "T", which supposed to be in REF column. The program somehow missed a "\t" due to lack of content for "ID" column. Is this normal or a bug? This gave me trouble when I try to read the vcf file (I can correctly read the vcf file created by samtools SNP calls), since the column content shift between the columns. Also noticed that vcf file has 5 samples: Sample1 Sample2 Sample3 Sample4 Sample5, even if I have give the 5 samples' bam files with names (F2, F3, etc) in my command, the program did not take them, but use anonymous names there, I wish the order is the same as what I listed there in my command, is that true? Thanks for your help! Ming Ming Yi (Contractor), Ph.D. Information System Program SAIC-Frederick, Inc. National Cancer Institute at Frederick Post Office Box B, Frederick, MD 21702 Phone: 301-846-5764 Fax: 301-846-7070 my...@nc... |
