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Forum: Bioinformatics 04-28-2015, 08:29 PM
Replies: 11
Views: 3,976
Posted By d3d1y
The problem is that --output-vcf 1 doesn't work...

The problem is that --output-vcf 1 doesn't work for pileup2snp, it only works for mpileup2snp. Lack of documentation for this flag, plus lack of error checking for command line args, makes it hard to...
Forum: Bioinformatics 04-27-2015, 08:27 PM
Replies: 11
Views: 3,976
Posted By d3d1y
Yep. Me too. Exactly the same situation: illumina...

Yep. Me too. Exactly the same situation: illumina fastq to bam via bwa; samtools mpileup to vcf via varscan --output-vcf. Resulting vcf has no header.
Latest Ubuntu, latest samtools, latest varscan...
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