VarScan Discussion

Variant detection in next-generation sequencing data

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VCF format for pileup2snp By Shihua Dong on Fri Jun 28, 2024 05:13 PM	1	121	By Shihua Dong on Fri Jun 28, 2024 05:13 PM
mpileup2somatic - high confidence calls with processSomatic By Ester on Mon May 13, 2024 10:23 AM	1	130	By Ester on Mon May 13, 2024 10:23 AM
fpfilter --min-var-count By Ester on Mon May 13, 2024 10:01 AM	1	89	By Ester on Mon May 13, 2024 10:01 AM
fpfilter --min-var-count By Ester on Mon May 13, 2024 10:01 AM	1	72	By Ester on Mon May 13, 2024 10:01 AM
too much memory usage By Natalie Saini on Wed Jun 29, 2022 03:08 PM	1	173	By Natalie Saini on Wed Jun 29, 2022 03:08 PM
VarScan compare parsing (Warning: Unable to parse chrom/position from... By Jess Buddle on Tue May 31, 2022 02:45 PM	1	232	By Jess Buddle on Tue May 31, 2022 02:45 PM
File Parsing Exception with either process substitution or pipe By Melissa Chua on Tue Apr 12, 2022 12:09 PM	2	217	By Dan Koboldt on Tue Apr 12, 2022 12:44 PM
refArmSize file By rk2802 on Tue Feb 08, 2022 11:23 AM	1	205	By rk2802 on Tue Feb 08, 2022 11:23 AM
mpileup2cns fails when mpileup has no output By Michael Yourshaw on Tue Nov 23, 2021 12:06 AM	1	178	By Michael Yourshaw on Tue Nov 23, 2021 12:06 AM
varscan readcounts command By Gianfilippo Coppola on Sat Oct 19, 2019 02:35 AM	3	461	By Dan Koboldt on Thu Sep 30, 2021 01:03 PM
ambiguous call from VarScan By Hubert DENISE on Wed Sep 22, 2021 04:53 PM	1	193	By Hubert DENISE on Wed Sep 22, 2021 04:53 PM
fpfilter: all variants failed because no readcounts were returned By vic on Thu Nov 19, 2020 03:09 AM	13	1013	By Vanessa Souza on Tue May 11, 2021 04:17 PM
fpfilter.pl - failed to get readcounts for variant allele By Vanessa Souza on Mon May 10, 2021 02:51 PM	1	262	By Vanessa Souza on Mon May 10, 2021 02:51 PM
How does Varscan somatic classify the INFO/SS tag for somatic status By Brian Wiley on Wed Mar 24, 2021 04:12 PM	1	238	By Brian Wiley on Wed Mar 24, 2021 04:12 PM
somaticFilter By KELLY L BOLTON on Mon Mar 15, 2021 09:31 PM	1	221	By KELLY L BOLTON on Mon Mar 15, 2021 09:31 PM
Varscan Somatic VCF Output By Brian Wiley on Fri Mar 12, 2021 09:51 PM	6	587	By Brian Wiley on Sat Mar 13, 2021 08:40 PM
--output-vcf 1 option disabled --strand-filter? By vic on Tue Dec 22, 2020 12:27 AM	1	239	By vic on Tue Dec 22, 2020 12:27 AM
how to report monomorphic position By liweiguo1 on Fri Sep 04, 2020 03:52 AM	1	260	By liweiguo1 on Fri Sep 04, 2020 03:52 AM
varscan somatic with one combined input, but the command expects 2 in... By Ye Tian on Wed Aug 05, 2020 04:28 PM	1	275	By Ye Tian on Wed Aug 05, 2020 04:28 PM
Malformed VCF output 2 By Jose Fernandez on Mon Aug 03, 2020 10:57 AM	1	225	By Jose Fernandez on Mon Aug 03, 2020 10:57 AM
how to calculate MinMMQSdiff By Yongzhe Ren on Mon Jul 27, 2020 01:05 AM	1	400	By Yongzhe Ren on Mon Jul 27, 2020 01:05 AM
Malformed VCF output By Jose Fernandez on Tue Jul 21, 2020 09:36 AM	5	466	By Jose Fernandez on Wed Jul 22, 2020 08:14 AM
Tumor purity option By Yuyu Liu on Mon Jul 13, 2020 02:46 AM	3	237	By Yuyu Liu on Wed Jul 15, 2020 06:08 AM
Compatibility with Nanopore data By Jonathan on Tue Apr 21, 2020 09:22 AM	1	348	By Jonathan on Tue Apr 21, 2020 09:22 AM
freq is inconsistently calculated as a function of DP, AD, and RD By Brandon on Fri Feb 21, 2020 06:36 PM	2	392	By Dan Koboldt on Fri Feb 21, 2020 08:38 PM

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