Hello,
I am performing an analysis for SNPs in Galaxy UCSC, using the tools mpileup (to generate pileup from bam files) and Varscan (to generate vcf from pileup files).
Although the programs work fine, I haven't been able to find a way to add the column with + and - at the final vcf file, in order to show on which strand does the reported reference base and alternative base belong.
Is there a step before the analysis or after (etc the annotation) from where I can extract this information?
Kostas
I am performing an analysis for SNPs in Galaxy UCSC, using the tools mpileup (to generate pileup from bam files) and Varscan (to generate vcf from pileup files).
Although the programs work fine, I haven't been able to find a way to add the column with + and - at the final vcf file, in order to show on which strand does the reported reference base and alternative base belong.
Is there a step before the analysis or after (etc the annotation) from where I can extract this information?
Kostas
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