A question on GetPileupSummaries (GATK)
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2.2 years ago
Laven9 • 0

I am confusing what "common_biallelic.vcf.gz" is? Am I right if I run it like this:

 gatk SelectVariants \
-R Homo_sapiens_assembly38.fasta \
--restrict-alleles-to biallelic \
-O common_biallelic.vcf.gz


Or should I change the -V for something else like my normal.vcf?

GetPileupSummaries • 1.3k views
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Hey, I don't think you should use your normal.vcf. Here dbSNP site has common_all_xxx.vcf.gz , also I think GATK bundle will provide common variant file.

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Thank you, MatthewP ! But as I am new in the field, could you please tell me how to interpret the file common_all_xxx.vcf.gz? If it is right that in my opinion, it should be a file containing all the common snps in a large group of people, so that gatk4 could use it to exclude those snps in the Mutect2.output.file?