Mercurial > repos > chrisw > monorail_test
comparison monorail.sh @ 5:d2d9937d1f9c draft
Uploaded
| author | chrisw |
|---|---|
| date | Tue, 12 Feb 2019 13:51:52 -0500 |
| parents | ae546ad6f2f4 |
| children |
comparison
equal
deleted
inserted
replaced
| 4:ae546ad6f2f4 | 5:d2d9937d1f9c |
|---|---|
| 27 samtools sort -T ./samtools_temp -@ $threads -m 64M -o $sorted_bam $sout > stools.log 2>&1 | 27 samtools sort -T ./samtools_temp -@ $threads -m 64M -o $sorted_bam $sout > stools.log 2>&1 |
| 28 #index | 28 #index |
| 29 samtools index -@ $threads $sorted_bam >> stools.log 2>&1 | 29 samtools index -@ $threads $sorted_bam >> stools.log 2>&1 |
| 30 | 30 |
| 31 #get coverage summaries | 31 #get coverage summaries |
| 32 bamcount $sorted_bam --threads $threads --coverage --no-head --require-mdz --min-unique-qual $min_uniq_qual --frag-dist bc --bigwig bc --annotation $annotation bc --auc bc --lats bc > bc.log 2>&1 | 32 bamcount $sorted_bam --threads $threads --coverage --no-head --require-mdz --min-unique-qual $min_uniq_qual --frag-dist bc --bigwig bc --annotation $annotation bc --auc bc --alts bc > bc.log 2>&1 |