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SelectVariants is not recognizing a sample by name

juandencisojuandenciso BogotaMember
edited March 2017 in Ask the GATK team

Hi, I'm having a strange error when using the SelectVariants tool; when I try to extract one sample from a multi sample vcf (which I'm sure includes the sample) I get the following error message:

###### ERROR MESSAGE: Bad input: Samples entered on command line (through -sf or -sn) that are not present in the VCF.

I also have an individual .g.vcf for this sample and when trying to extract it from this file, same error.

Here is the command line I used to perform the last test I mentioned:

java -Xmx2g -jar /path/to/GATK/GenomeAnalysisTK.jar -T SelectVariants -R /path/to/reference.fasta -V 2076.raw.snps.indels.g.vcf -o try_2076_sample.vcf -sn HC.2076

When checking the #CHROM line for this .g.vcf file I get the following:

grep CHROM 2076.raw.snps.indels.g.vcf
#CHROM POSID REF ALT QUAL FILTER INFO FORMAT HC.2076

So there's the sample and it still fails to detect it.

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