Multisample variant Processing

Question

[ruavol.bb]

I have a 928 non related vcd sample file. It has been annotated with appropriate RSID's. How do I query the file for the sample along with the correspond ID? Analysis requires the sample name the ref/alt allele and the RSID number. If I use vcd-subset, I get them sample but not the ID. Thanks for any directions.

[ruavol.bb]

Thanks for the awk command. The problem I ran into is that the RSID information is in the INFO field. I need it in the ID column so when I query by sample I have the rs associated with that position. I also tried the GATK and output was 0 records processed. I also tried bcftools query and it is close but no line by sample.

Answer 1

[Pierre Lindenbaum]

gunzip -c input.vcf.gz |  awk -F '\t' '($0 ~ /^#/ || $3=="rs1234")'

?

or GATK selectvariants with --keepIDs https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php#--keepIDs

--keepIDs / -IDs

List of variant IDs to select

If a file containing a list of IDs is provided to this argument, the tool will only select variants whose ID field is present in this list of IDs. The matching is done by exact string matching. The expected file format is simply plain text with one ID per line.