slzhao/QC3

Bug report

Opened this issue · 4 comments

shanj-github commented

vcfSummary.pm can not parse my vcf file properly. Command: perl qc3.pl -m v -i test.vcf -o my-out-dir. It always gives a lot of errors like "Use of uninitialized value ... ...", then causes R functions crash (non-numeric values passed to numeric variables ...). Please let me know if you need my test.vcf to do debug, thanks!

shanj-github commented

I tried qc3 version 1.20 and 1.32, got similar errors.

slzhao commented

Hello,

VCF QC in QC3 is designed for vcf files generated by GATK. Vcf files
generated by other software, such as MuTect is not supported yet. If your
vcf file is generated by GATK, please send it to me so that I can fix the
issue.

Best,
Shilin

2015-09-14 9:18 GMT-05:00 shanj-github notifications@github.com:

I tried qc3 version 1.20 and 1.32, got similar errors.

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#2 (comment).

shanj-github commented

Hi Shilin,

Thank you for your quick response. I’m in contact with the user who provides the file to confirm if the file generated by GATK.
Will let you know shortly, thanks again!

Jigui Shan
Bioinformatics Analyst
Frederick National Laboratory for Cancer Research
Leidos Biomedical Research, Inc.
P.O. Box B. Frederick, MD 21702
Phone: 301-846-5157
shanj@mail.nih.gov

On 9/14/15, 10:25 AM, "slzhao" notifications@github.com wrote:

Hello,

VCF QC in QC3 is designed for vcf files generated by GATK. Vcf files
generated by other software, such as MuTect is not supported yet. If your
vcf file is generated by GATK, please send it to me so that I can fix the
issue.

Best,
Shilin

2015-09-14 9:18 GMT-05:00 shanj-github notifications@github.com:

I tried qc3 version 1.20 and 1.32, got similar errors.

—
Reply to this email directly or view it on GitHub
#2 (comment).

—
Reply to this email directly or view it on GitHub #2 (comment) .

shanj-github commented

Hi Shilin,

My vcf file was generated by MuTect. I’ll let you know in case we run into any issues with vcf files from GATK.

Thank you!

Jigui Shan
Bioinformatics Analyst
Frederick National Laboratory for Cancer Research
Leidos Biomedical Research, Inc.
P.O. Box B. Frederick, MD 21702
Phone: 301-846-5157
shanj@mail.nih.gov

On 9/14/15, 10:25 AM, "slzhao" notifications@github.com wrote:

Hello,

VCF QC in QC3 is designed for vcf files generated by GATK. Vcf files
generated by other software, such as MuTect is not supported yet. If your
vcf file is generated by GATK, please send it to me so that I can fix the
issue.

Best,
Shilin

2015-09-14 9:18 GMT-05:00 shanj-github notifications@github.com:

I tried qc3 version 1.20 and 1.32, got similar errors.

—
Reply to this email directly or view it on GitHub
#2 (comment).

—
Reply to this email directly or view it on GitHub #2 (comment) .