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Squash SAMTools stderr chatter when using FreeBayes which would cause error state. FreeBayes should be updated to e.g. have access to built-in reference genomes, etc.

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This commit is contained in:
Daniel Blankenberg
2011-11-08 10:59:27 -05:00
parent 8a1585a4bb
commit 1284227acd
1 changed files with 5 additions and 5 deletions
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tools/human_genome_variation/freebayes.xml
+5 -5
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@@ -5,11 +5,11 @@
</requirements>
<description>Bayesian genetic variant detector</description>
<command>
ln -s $reference localref.fa;
ln -s $bamfile localbam.bam;
samtools faidx localref.fa;
samtools sort localbam.bam localbam.bam;
samtools index localbam.bam;
ln -s $reference localref.fa &amp;&amp;
ln -s $bamfile localbam.bam &amp;&amp;
samtools faidx localref.fa 2&gt;&amp;1 || echo "Error running samtools faidx for FreeBayes" &gt;&amp;2 &amp;&amp;
samtools sort localbam.bam localbam.bam 2&gt;&amp;1 || echo "Error running samtools sort for FreeBayes" &gt;&amp;2 &amp;&amp;
samtools index localbam.bam 2&gt;&amp;1 || echo "Error running samtools index for FreeBayes" &gt;&amp;2 &amp;&amp;
freebayes --fasta-reference localref.fa localbam.bam --vcf $output
#if $params.source_select == "full":
$params.showRefRepeats