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gatk SelectVariants odd behavior
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15 months ago

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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