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 \
 -V gnomad.vcf.gz \
 --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?

BTW, sorry to use the answer section, my "add reply" is out of work.

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