#1 VCF format specifics

[LStead]

Hi. Please could the VCF format used in the CHAT programme, and the code given for extracting LRR and BAF from sequencing data, be confirmed? I have variants called using VarScan2 and I do not have a VCF file so I need to parse my data into the right format. As previously noted, there seems to be some differences in VCF so I need the exact format for CHAT
Thank you

[Bo Li]

Hi, by default, CHAT accommodates the format used in TCGA:
https://tcga-data.nci.nih.gov/tcga/dataAccessMatrix.htm. Specifically, the
10th and 11th columns are tumor and paired normal. Within 10th or 11th
column, allele depth (AD) should be the 2nd or 3rd field (you may specify
in the function getCCF). Hope that is clear.

On Fri, Oct 30, 2015 at 11:11 AM, LStead medlste@users.sf.net wrote:

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• [tickets:#1] http://sourceforge.net/p/clonalhetanalysistool/tickets/1/
  VCF format specifics*

Status: open
Milestone: 1.0
Created: Fri Oct 30, 2015 03:11 PM UTC by LStead
Last Updated: Fri Oct 30, 2015 03:11 PM UTC
Owner: Bo Li

Hi. Please could the VCF format used in the CHAT programme, and the code
given for extracting LRR and BAF from sequencing data, be confirmed? I have
variants called using VarScan2 and I do not have a VCF file so I need to
parse my data into the right format. As previously noted, there seems to be
some differences in VCF so I need the exact format for CHAT
Thank you

---

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[LStead]

Thank you

[LStead]

Hi again. I'm afraid that link does not work and I am stuggling a bit to understand the exact format that you have used given the apparent flexibility in the INFO and FORMAT columns for vcf files. Would you mind posting the header and maybe just 2-3 lines from a vcf file you have used in your pipeline just so I can be sure? Kind regards

[Bo Li]

Hi,

The first 3 lines of the VCF are like this:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL PRIMARY

1 14610 . T C 28 blq SS=1;VT=SNP;DP=7 GT:DP:AD:BQ:MQ:SB:FA
0/1:3:2,1:37.0,39.0:29.5,23.0:0.0,0.0:0.333
0/1:4:2,2:39.5,40.0:22.5,23.0:0.0,0.0:0.5

1 14677 . G A 8 q10;bldp;blq SS=1;VT=SNP;DP=14 GT:DP:AD:BQ:MQ:SB:FA
1/0:2:2,0:37.5,0:23.0,0:0.0,0:0.0
1/0:12:9,3:36.8,36.7:22.9,22.0:0.333,0.333:0.25

Hope that helps,

Bo

On Thu, Nov 12, 2015 at 10:00 AM, LStead medlste@users.sf.net wrote:

Hi again. I'm afraid that link does not work and I am stuggling a bit to
understand the exact format that you have used given the apparent
flexibility in the INFO and FORMAT columns for vcf files. Would you mind
posting the header and maybe jst 2-3 ines form a vcf file you have used in
your pipeline just so I can be sure? Kind regards

---

• [tickets:#1] http://sourceforge.net/p/clonalhetanalysistool/tickets/1/
  VCF format specifics*

Status: open
Milestone: 1.0
Created: Fri Oct 30, 2015 03:11 PM UTC by LStead
Last Updated: Fri Oct 30, 2015 03:11 PM UTC
Owner: Bo Li

Hi. Please could the VCF format used in the CHAT programme, and the code
given for extracting LRR and BAF from sequencing data, be confirmed? I have
variants called using VarScan2 and I do not have a VCF file so I need to
parse my data into the right format. As previously noted, there seems to be
some differences in VCF so I need the exact format for CHAT
Thank you

---

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