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  • Samtools: Information about percentages in SAM files

    Hi,

    I have used BWA mem to map paired-end reads to different references.
    I am looking for mapped and unmapped reads percentages (e.g. mapped reads 96 %) and I don't know if samtools has such an option.

    I actually know that this command line here

    samtools view -c -f 4 -S filename.sam

    outputs the unmapped reads and with a capital (-F) the number of mapped reads. Do I have to calculate the percentages by my own or is there a fancy option in samtools ?

    Best,
    Flo

  • #2
    Look into "idxstats" option for samtools for getting the information you want. If you need visual graphs and such you can look at Qualimap.

    Also this (cut -f2 for mapped reads and cut -f3 for unmapped): http://seqanswers.com/forums/showthr...3744#post53744 and the explanation here: https://www.biostars.org/p/14569/

    Smatools "flagstat" will provide aggregate information: https://www.biostars.org/p/84396/
    Last edited by GenoMax; 10-08-2015, 05:32 AM.

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