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
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written
by
jon.klonowski
1 answer
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!
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