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Pileup To Vcf Format

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

pileup vcf
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updated by Mbillah Mbillah • written by Pri • Pri

1 answer

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.
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written by Pierre Lindenbaum Pierre Lindenbaum

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??

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written by Pri • Pri

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??

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written by Pri • Pri

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?? – pri 0 secs ago

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written by Pri • Pri

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??

• 0 views • link
written by Pri • Pri

could you suggest anything else??

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written by Pri • Pri

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

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written by Chris Evelo Chris Evelo

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