Error while running QC3: vcf QC

[shalabhsuman]

Hello,

I was testing out the "vcf QC" module with out test VCF data, and I am getting the following errors:

Use of uninitialized value $allele1 in string ne at...
Argument "." isn't numeric in addition (+) at..
Use of uninitialized value $allele1 in numeric gt (>) at...

Any comments??

Thanks,

Shalabh

P.S. The VCF file is multi-sample VCF.

[slzhao]

Hello Shalabh,

QC3 supports vcf files generated by GATK, including multi-sample VCF. Your
vcf file may have a different format.
You can compare your vcf file with QC3 example vcf file. Or you can send me
part of your vcf file so that I can check it and let you know the reason.

Best,
Shilin

2015-04-14 17:11 GMT-05:00 shalabhsuman notifications@github.com:

Hello,

I was testing out the "vcf QC" module with out test VCF data, and I am
getting the following errors:

Use of uninitialized value $allele1 in string ne at...
Argument "." isn't numeric in addition (+) at..
Use of uninitialized value $allele1 in numeric gt (>) at...

Any comments??

Thanks,

Shalabh

P.S. The VCF file is multi-sample VCF.

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[shalabhsuman]

Thanks, Shilin. Would it be alright if I email you the test VCF data??

[slzhao]

Sure. I think some lines from your vcf file is enough.

Best,
Shilin

2015-04-14 17:26 GMT-05:00 shalabhsuman notifications@github.com:

Thanks, Shilin. Would it be alright if I email you the test VCF data??

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[shalabhsuman]

Shilin- can you provide me with your email address information, so I can share with you some of the VCF data. Thanks.

[slzhao]

Please email me: zhaoshilin@gmail.com

2015-04-15 9:09 GMT-05:00 shalabhsuman notifications@github.com:

Shilin- can you provide me with your email address information, so I can
share with you some of the VCF data. Thanks.

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[slzhao]

Based on your test file, there are some SNPs labeled as "./.:.:1", which
was not supported by QC3.
I've updated a newer version to support it. You can use it now.

Best,
Shilin

2015-04-15 9:50 GMT-05:00 zhao shilin zhaoshilin@gmail.com:

Please email me: zhaoshilin@gmail.com

2015-04-15 9:09 GMT-05:00 shalabhsuman notifications@github.com:

Shilin- can you provide me with your email address information, so I can
share with you some of the VCF data. Thanks.

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[slzhao]

Hello Shalabh,
I've updated a new version (1.25) for your new test file (
ensembled_variant_part_bba.vcf). It will work now.

Best,
Shilin

2015-04-16 0:24 GMT-05:00 zhao shilin zhaoshilin@gmail.com:

Based on your test file, there are some SNPs labeled as "./.:.:1", which
was not supported by QC3.
I've updated a newer version to support it. You can use it now.

Best,
Shilin

2015-04-15 9:50 GMT-05:00 zhao shilin zhaoshilin@gmail.com:

Please email me: zhaoshilin@gmail.com

2015-04-15 9:09 GMT-05:00 shalabhsuman notifications@github.com:

Shilin- can you provide me with your email address information, so I can
share with you some of the VCF data. Thanks.

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[shalabhsuman]

Hi Shilin,

Thank you so much for looking into this for us. I did run the latest version and test it out with our VCF data including the test file "ensembled_variant_part_bba.vcf", and before the analysis would finish, I received the following log (Screenshot attached):

Please let me know your thoughts on this.

Thanks again,

Shalabh

[slzhao]

Hello Shalabh,

I double checked your vcf file and found it had mixed formats. For example,
line 124 has GT:DP:PL while line 123 has GT:AD:DP:GQ:PL. It is not
supported by QC3.

So that QC3 reads some of the data incorrectly and reports some error.

Best,
Shilin

2015-04-20 15:35 GMT-05:00 shalabhsuman notifications@github.com:

Hi Shilin,

Thank you so much for looking into this for us. I did run the latest
version and test it out with our VCF data including the test file
"ensembled_variant_part_bba.vcf", and before the analysis would finish, I
received the following log (Screenshot attached):

[image: screen shot 2015-04-20 at 4 34 15 pm]
https://cloud.githubusercontent.com/assets/4998368/7239867/26a022b4-e77b-11e4-986b-cbcf937436c9.png

Please let me know your thoughts on this.

Thanks again,

Shalabh

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[slaurie]

Hi Shilin,

I like your tool, though I haven't actually tried to run it yet. However, seeing what you say above, I think you may run into trouble with VCF files produced by GATK haplotype caller, as they typically have two different lengtgs of format field - the 5 you mention above, and 2 extra fields if it detects a haplotype (PGT and PID) and produces a phased call. While you can switch off this extra formatting when you perform your initial calling, since it can be informative it is not likely that people will do so.

If I can find the time to test your tool I'll confirm if my suspicion is correct.

All the best, Steve

[slzhao]

Hi Steve,

Thanks for your reminder. I am using QC3 in my new project in these days
and I will update it if I change the codes.

Best,
Shilin

2016-01-28 7:45 GMT-06:00 slaurie notifications@github.com:

Hi Shilin,

I like your tool, though I haven't actually tried to run it yet. However,
seeing what you say above, I think you may run into trouble with VCF files
produced by GATK haplotype caller, as they typically have two different
lengtgs of format field - the 5 you mention above, and 2 extra fields if it
detects a haplotype (PGT and PID) and produces a phased call. While you can
switch off this extra formatting when you perform your initial calling,
since it can be informative it is not likely that people will do so.

If I can find the time to test your tool I'll confirm if my suspicion is
correct.

All the best, Steve

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