Hi,
Is there some tool that allows extracting positions based on 4 columns, not based on 2 columns? Like in tabix, to get coordinates like
chrom=10 pos=1001 ref=A alt=G
I need to firstly exectue:
tabix myTabFile.gz 10:1000-1001
and then I need to iterate and parse the results.
Is there some tool so I could extract the data directly? like
someTools myTabFile.gz 10:1001:G:A
??
Yes, I'm interested in parsing VCF files or some big tables that have columns chrom, pos, ref, alt (like dbNSFP).
Thanks!
•
written
by
damian.loska •
pipe into awk according to your input syntax. Something like
tabix myTabFile.gz 10:1000-1001 | awk '($3=="A" && $4=="G")'
yeah, but this is still "some parsing" (I use python, pysam... subprocess would be additonal overhead). Hmmm... I'll try to format a file like:
chrom_ref_alt pos the rest of anns
like
10_A_G 1001 DP RD AF
10_T_C 1002 DP RD AF
and then to use tabix...
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