Entering edit mode
19 months ago
TraPS-VarI
•
0
The following is a command to query a single mutation in FGFR4 -->"FGFR4\tG388R" using jvarkit
echo -e "FGFR4\tG388R" | java -jar dist/backlocate.jar -R hg19.fa --gtf Homo_sapiens.GRCh37.87.gtf
The output is as follows:
FGFR4 Gly 388 Arg FGFR4 ENST00000292408 + G 1161 GGG AGG|CGG G chr5 176520242 ENST00000292408.Exon9 . .
FGFR4 Gly 388 Arg FGFR4 ENST00000292408 + G 1162 GGG AGG|CGG G chr5 176520243 ENST00000292408.Exon9 . .
FGFR4 Gly 388 Arg FGFR4 ENST00000292408 + G 1163 GGG AGG|CGG G chr5 176520244 ENST00000292408.Exon9
. .
I am unable to figure a way to query a long list containing thousands of mutations. Can anyone please suggest a way to query the list (containing ~1000s mutations) (as -i infile
) instead of individual mutations? Thanks
Here is the solution as suggested by the @lindenb
where input_list contains
ICOS\tF141X CDH10\tL614X KCNE2\tV49X MMP24\tV603X