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Since we want a binary .bam as output, but bwa samse (and sampe) produce .sam text output, we pipe the .sam file output to samtools view to convert it to .bam output, which is then redirected to an output file named using the user's output prefix. This command chaining or "piping" avoids having to write then read an intermediate .sam file. Note the dash on the samtools view -b -S - command line means samtools should look for its input data on standard input instead of in a file.
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samtools flagstat $OUT_PFX.sorted.bam | tee $OUT_PFX.flagstat.txt ckRes $? "samtools flagstat"; ckFileSz "$OUT_PFX.flagstat.txt"; |
Note we tee the output so that the information is both stored in a file and appears in the execution log. Output from samtools flagstat looks like this for paired end alignments:
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