bioawk

1. bioawk -c help

bed:
1:chrom 2:start 3:end 4:name 5:score 6:strand 7:thickstart 8:thickend 9:rgb 10:blockcount 11:blocksizes 12:blockstarts
sam:
1:qname 2:flag 3:rname 4:pos 5:mapq 6:cigar 7:rnext 8:pnext 9:tlen 10:seq 11:qual
vcf:
1:chrom 2:pos 3:id 4:ref 5:alt 6:qual 7:filter 8:info
gff:
1:seqname 2:source 3:feature 4:start 5:end 6:score 7:filter 8:strand 9:group 10:attribute
fastx:
1:name 2:seq 3:qual 4:comment

2. flag 为2，且第六列包含D输出

samtools view -f 2 demo.bam | awk '$6 ~ /D/ { print $6 }' | head
samtools view -f 2 demo.bam | bioawk -c sam '$cigar ~ /D/ { print $cigar }' | head