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Problem With Mpileup

I tried to make a coverage per base figure by processing single_reference.sam file with following commands:; samtools view -bS $1.sam > $1.bam; samtools sort $1.bam > $1.sort.bam; samtools mpileup $1.sort.bam > $1.c; cat $1.c | awk '{FS=" "}{print $2" "$4}' > $1.pileup

However, I received the following notice after running the sh:; [samopen] SAM header is present: 1 sequences.; Usage: samtools sort [-on] [-m <maxMem>] <in.bam> <out.prefix>; [bamheaderread] bgzfcheckEOF: Invalid argument; [bamheaderread] invalid BAM binary header (this is not a BAM file).; sam2bam2pileup.sh: line 4: 24893 Segmentation fault samtools mpileup $1.sort.bam > $1.c

Thanks for your gracious help!

samtools mpileup sam bam
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updated by Anders Bergström • Anders Bergström • written by virtuouslycan • virtuouslycan

1 answer

Samtools sort doesn't write to standard output, rather it writes to a file for which you specify the name prefix as an argument (samtools will add the ".bam" extension itself):

samtools sort inputFile.bam outputFile

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written by Anders Bergström • Anders Bergström

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