gatk SelectVariants odd behavior

Question

[jon.klonowski]

gatk SelectVariants is not working properly for me...

I have a file of SNP ids (i.e chr1:861219:G:C) delimited with /n and a vcf where the snp ID is also formatted chr:pos:ref:alt (chr1:861219:G:C).

The list file of SNPs were generated by subsetting a portion of the vcf SNPs (based on 1000G frequency) when I try:

gatk SelectVariants --variant File_name.vcf.gz -O Output_file_name.vcf.gz --keep-ids SNPS_of_interest.txt

I get a file of just the headers.

and then when I try:

 gatk SelectVariants --variant File_name.vcf.gz -O Output_file_name.vcf.gz --exclude-ids SNPS_of_interest.txt

The output is the same as the input excluding a zless | wc -l of ~10

[Kevin Blighe]

You may want to post on the GATK Support Forum.

Answer 1

[cricgpu]

Although not explicitly stated in the gatk SelectVariants docs, make sure your filtering files have the suffix .list. In you example change SNPS_of_interest.txt to SNPS_of_interest.list. This also hold true for other filters eg. --keepIDs.

Hope this helps!