Question

Pileup To Vcf Format

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13.0 years ago

Pri ▴ 20

I have a pileup file generated using samtools. I need to convert this to vcf. Which tools can be used for this??

pileup vcf • 9.5k views

ADD COMMENT • link updated 5.4 years ago by Mbillah ▴ 140 • written 13.0 years ago by Pri ▴ 20

score 3 · Answer 1 · 2011-04-15

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13.0 years ago

Pierre Lindenbaum 161k

there is a tool named sam2vcf.pl in the misc folder of samtools

Usage: sam2vcf.pl [OPTIONS] < in.pileup > out.vcf
Options:
   -r, -refseq <file.fa>            The reference sequence, required when indels are present.
   -h, -?, --help                   This help message.

ADD COMMENT • link 13.0 years ago by Pierre Lindenbaum 161k

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Well I don't see an -s option in that usage description just a < to specify the input.

ADD REPLY • link 13.0 years ago by Chris Evelo 10k

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I tried this several times but i m getting this error:

C:wishsamtools-0.1.15misc>perl sam2vcf.pl -s hg19_bwa_target2.pileup > out.vcf Unknown parameter "hg19_bwa_target2.pileup". Run -h for help. at sam2vcf.pl line 22 main::error('Unknown parameter "hg19_bwa_target2.pileup". Run -h for hel p.x{a}') called at sam2vcf.pl line 52 main::parse_params() called at sam2vcf.pl line 12

What might be my mistake here??

ADD REPLY • link 13.0 years ago by Pri ▴ 20

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could you suggest anything else??

ADD REPLY • link 13.0 years ago by Pri ▴ 20