Mercurial > repos > jjohnson > pileup_to_vcf
diff pileup_to_vcf.xml @ 2:d6de2d1f4af9
Fix read depth reporting
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Sun, 03 Mar 2013 20:38:43 -0600 |
parents | 3890f8ba0e4d |
children | fafa105e5f58 |
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--- a/pileup_to_vcf.xml Mon Feb 18 19:11:47 2013 -0600 +++ b/pileup_to_vcf.xml Sun Mar 03 20:38:43 2013 -0600 @@ -60,9 +60,10 @@ help="Multiple alleles may be output in the VCF if the allowable frequency is below 0.5, otherwise only one will be reported"/> <param name="snps_only" type="boolean" truevalue="-s" falsevalue="" chacked="false" label="Only report SNPs, not indels" /> <param name="depth_as" type="select" label="Report DP and SAF with read coverage of" help="The reported read voverage depth: DP, and the calculation of specific allele frequency (SAF) of variants"> - <option value="ref" selected="true">Reads at this position</option> + <option value="source">Read coverage reported in pileup</option> + <option value="ref" selected="true">Reads at this position that have a base call</option> <option value="qual">Reads at this position taht pass the base call quality threshold</option> - <option value="all"></option> + <option value="all">All reads and indels</option> </param> </inputs> <outputs>