VCF output bugs.

[GoogleCodeExporter]

1. AD field not properly computed.(It is always two identical number)
2  Header for PSOM, incorrectly defined it as an Integer
3. Most headers for fields in the "INFO" section are incorrectly defined as 
"FORMAT" instead of ID... OR they were meant to be in the genotype field (they 
are sample specific) .. and were incorrectly assigned to the INFO field. For 
example, the PSOM field really should be a FORMAT (as it is), but the value 
should be reported in the genotype field and not the info fields.
4. there is a GQ field defined in the header as a FORMAT, but it is not 
populated in the VCF's genotype field.

What is the expected output? What do you see instead?

What version of the product are you using? On what operating system?

Please provide any additional information below.

Original issue reported on code.google.com by doyou...@gmail.com on 12 Jun 2012 at 2:11

[GoogleCodeExporter]

I am not sure I understand this. The software does not output to vcf.

Original comment by AndrewJL...@gmail.com on 12 Jun 2012 at 4:09

[GoogleCodeExporter]

I take back item 1.
" AD field not properly computed.(It is always two identical number)"
This is actually a bug in GATK Somatic Indel Detector... which we concatenate 
to the output of joint SNV mix.

Original comment by doyou...@gmail.com on 12 Jun 2012 at 6:55

[GoogleCodeExporter]

I am closing this as JointSNVMix does not create VCF files. If this is a 
feature request a new issue could be opened requesting VCF support.

Original comment by AndrewJL...@gmail.com on 8 Dec 2012 at 7:52

• Changed state: Invalid