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Code Block
languagebash
module load biocontainers  # takes a while
module load samtools

cd $SCRATCH/core_ngs/alignment/samtools
samtools view yeast_pe.sort.bam | head

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Code Block
languagebash
cd $SCRATCH/core_ngs/alignment/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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