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Sometimes you just want to examine a subset of reads in detail. Once you have a sorted and indexed BAM, you can use the coordinate filtering options of samtools view to do this. Here are some examples:
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When you're interested in mapped reads (which is true most of the time) be sure to specify the -F 0x4 option, which says to filter records where the 0x4 flag (read unmapped) is 0, resulting it only mapped reads being output. |
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# if needed... cd $SCRATCH/core_ngs/alignment/samtools module load samtools # count the number of reads mapped to chromosome 2 (chrII) samtools view -c -F 0x4 yeast_pe.sort.bam chrII # count the number of reads mapped to chromosomes 1 or M (chrI, chrM) samtools view -c -F 0x4 yeast_pe.sort.bam chrI chrM # count the number of reads mapped to chromosomes 1 that overlap coordinates 1000-2000 samtools view -c -F 0x4 yeast_pe.sort.bam chrI:1000-2000 # since there are only 20 reads in the chrI:1000-2000 region, examine them individually samtools view -F 0x4 yeast_pe.sort.bam chrI:1000-2000 # look at a subset of field for chrI:1000-2000 reads # 2=flags, 3=contig, 4=start, 5=mapping quality, 6=CIGAR, 9=insert size samtools view -F 0x4 yeast_pe.sort.bam chrI:1000-2000 | cut -f 2-6,9 |
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