A little command-line tool to process clinvar.vcf together with AncestryDNA.txt.
The tool filters clinvar.vcf on GENEINFO and then matches up all AncestryDNA.txt entries which refer to that rsID. For each match it outputs a combined line to stdout. It also parses the INFO part of the clinvar.vcf line.
Matching lines are at the end written to the file "filtered-DNA.json" in JSON format, which can be read with other tools, such as python pandas.
An initial commit with a command-line utility that takes a few arguments and filters the rsID list in AncestryDNA.txt and outputs matching data from clinvar.vcf.
Output all rsIDs where GENEINFO begins with MTHFR:
clinvar-ancestry clinvar.vcf AncestryDNA.txt --gene "MTHFR.*"
Output rsIDs where the clinvar GENEINFO begins with CBS or MTHFR and at least one allele in the AncestryDNA.txt entry is different from the REF allele:
clinvar-ancestry clinvar.vcf AncestryDNA.txt --gene "(CBS|MTHFR).*" --discrepancies
--gene <regex> : Output only rsIDs related to entries where GENEINFO matches this regex.
--discrepancies : Output only heterozygous or homozygous rsIDs.
--unmatched-rsid : Output also entries where there is no matching rsID in the clinvar.vcf.