bcftools select sites with multiple combinations of FILTER column
Hello
I would like to keep the rows that have the combinations of these expressions
bcftools query -i "%FILTER='PASS' | %FILTER='haplotype' | %FILTER='germline' | %FILTER='clustered_events'" -f '%CHROM\t%POS\t%REF\t%ALT[\t%AF]\n' invcf > outvcf
ie. `germline;clustered_events` ------> should be kept
but `germline;some_other_filter_not_listed` -------> should be eliminated
Is there a way to do this with bcftools?
1 answer
exclude/include:
bcftools view -e 'FILTER ~ "FILTER1"' -O u in.vcf | bcftools view -i 'FILTER ~ "FILTER2"' > out.vcf
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written
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Pierre Lindenbaum
use a first bcftools to exclude variants having filter FILTER1 and pipe into another bcftools to only include variants having FILTER2
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link
written
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Pierre Lindenbaum
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