Man pages for compbiocore/qckitalign
Quality Control for Mapped Reads

bam_readsReturns the number of distinct reads in the BAM file...
bam_recordsReturns the number of alignment records in the BAM file...
chimeric_proportionReturns proportion of reads that have been mapped to two...
chimeric_readsIdentifies reads by index record that have been mapped to two...
chimeric_rnameIdentifies reads with the same qname but different rname from...
chimeric_tagsIdentifies reads with the SA tag, indicating a chimeric read...
chromosomechromosome
cigar_partitioncigar partitioning
cigar_profcigar profile
cover_agecoverage rate: mean, median and sd
insert_sizeInsert size
map_quamapping quality
mult_mapmultiple mapping
num_chimericReturn number of chimeric reads from a bamfile.
unmapped_readsreturn name of unmapped reads
unq_mapunique mapping
compbiocore/qckitalign documentation built on July 3, 2018, 5:11 p.m.