Mercurial > repos > jeltje > samtools_1_18_mpileup
changeset 6:6757453c6af9 draft
Uploaded
author | jeltje |
---|---|
date | Mon, 12 Jan 2015 14:54:25 -0500 |
parents | ab1f85b31fe9 |
children | 0af969737b28 |
files | samtools_flagstat.xml |
diffstat | 1 files changed, 3 insertions(+), 2 deletions(-) [+] |
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--- a/samtools_flagstat.xml Mon Jan 12 14:52:17 2015 -0500 +++ b/samtools_flagstat.xml Mon Jan 12 14:54:25 2015 -0500 @@ -3,7 +3,7 @@ <requirement type="package" version="0.1.18">samtools</requirement> </requirements> <description>creates mpileup for VarScan2</description> - <command>samtools flagstat "$input1" "$input2" > "$output1" + <command>samtools mpileup "$input1" "$input2" > "$output1" </command> <inputs> <param name="input1" type="data" format="bam" label="BAM File" /> @@ -22,7 +22,8 @@ --> <help> -This tool runs the flagstat command of samtools 0.1.18 to produce simple stats on a BAM file. +This tool runs the mpileup command of samtools 0.1.18 +with flags -q 1 -B </help> </tool>