Mercurial > repos > gandres > vcftools_filter_stats_diversity
comparison VCFToolsStats/vcfToolsStats.sh @ 2:ac7c9e40d601 draft
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| author | gandres |
|---|---|
| date | Fri, 10 Jul 2015 04:16:17 -0400 |
| parents | |
| children | 612066e3f57d |
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| 1:0f67ed444d47 | 2:ac7c9e40d601 |
|---|---|
| 1 #!/bin/bash | |
| 2 | |
| 3 tool_path=$(dirname $0) | |
| 4 | |
| 5 filein=$1 | |
| 6 fileout_label=$2 | |
| 7 fileout_annot=$3 | |
| 8 fileout_het=$4 | |
| 9 fileout_imiss=$5 | |
| 10 fileout_sum=$6 | |
| 11 filelog=$7 | |
| 12 | |
| 13 | |
| 14 | |
| 15 perl $tool_path/VCFToolsStats.pl --input $filein --out $fileout_label | |
| 16 | |
| 17 cp $fileout_label.annotation $fileout_annot ; rm $fileout_label.annotation | |
| 18 cp $fileout_label.het $fileout_het ; rm $fileout_label.het | |
| 19 cp $fileout_label.imiss $fileout_imiss ; rm $fileout_label.imiss | |
| 20 cp $fileout_label.TsTv.summary $fileout_sum ; rm $fileout_label.TsTv.summary | |
| 21 | |
| 22 cp vcftools.log $filelog | |
| 23 rm vcftools.log |