Sam-stats computes statistics from (possibly compressed) SAM or BAM files. Some of the output statististics: mapped reads - if duplicate tracking was enabled via -D, it recapitulates the number of unique, mapped, probe-id*s in the original sam file. It is multiplied by 2 for paired-end data with duplicate read id*s. If you divide this by the number of reads in the fastq you aligned (possibly from the output of fastq-stats), you will get an accurate 'percentage of reads aligned' statistic. Pct ambiguous - 100
Parent program: ea-utils
Ea-utils is FASTQ processing utilities such as fastq-mcf, fastq-multx, fastq-join, varcall and sam-stats and other. These tools detect and remove sequencing adapters and primers, detect limited skewing at the ends of reads and clip, poor quality at the ends of reads and clip, discard sequences that are too short after all of the above, keep multiple mate-reads in sync while doing all of the above, merge overlapping paired-end reads and computing statisticsfrom SAM, BAM or Fasta files.