Question: Quick question: samtool idxstats and multiple mapping
0
gravatar for Aurelie MLB
5 months ago by
Aurelie MLB290
United Kingdom
Aurelie MLB290 wrote:

Hello,

A quick naive question please: Samtools idxstats outputs the number of reads mapped to a given reference sequence. Right? What does it do in case of multiple mapping please? Does it count the best alignment for a read or does it adds 1 to all reference sequences where it mapped? I could not find any detail in the documentation.

Many thanks

sequencing alignment • 260 views
ADD COMMENTlink modified 5 months ago by Devon Ryan78k • written 5 months ago by Aurelie MLB290
2

samtools idxstats outputs total mapped. If you would like to see secondary alignments, try flagstat from samtools. It would print secondary alignment.

ADD REPLYlink written 5 months ago by cpad01124.5k
1
gravatar for Devon Ryan
5 months ago by
Devon Ryan78k
Freiburg, Germany
Devon Ryan78k wrote:

As cpad0112 mentioned, every alignment is counted, whether secondary or supplementary. So if a read has multiple recorded alignments then each is counted.

BTW, this is only true of BAM files. For CRAM files on 0 will be returned.

ADD COMMENTlink modified 5 months ago • written 5 months ago by Devon Ryan78k

Thank you so much to both!! Really helpful!!

ADD REPLYlink written 5 months ago by Aurelie MLB290
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