Ignore Reads In Bwa

Question

[Ric]

Hello, Is there a way to ignore reads which can align in multiple position equally good using bwa?

Thank you in advance.

[Arun]

Optional flags in BWA, that is, XT:A:U flag in the sam file denotes unique read and XT:A:R denotes multiple mappings for that read. For paired-end reads, you might also want to consider the flag XT:A:M (one-mate recovered) which means that one of the pairs is uniquely mapped and the other isn't.

[Ric]

Thank you. Where did you get the flags from? I am interested on paired-end where both reads mapped unique. Which command have I to use?

[Arun]

I usually considered XT:A:U flag alone and discarded any other. But on seqanswers.com I came to know that people retain both XT:A:U and XT:A:M and removing any other read. So, I'd suggest that. If you're using perl, you can just use a regular expression just like that: if( $_ =~ /XT:A:U/ || $_ =~ /XT:A:M/ ) { print FILE_PTR $_ } else { next; }

[Arun]

Because you want both reads to be mapped uniquely (essentially all reads are mapped uniquely then), you can just use awk and regular expression as follows: awk '$0 ~ /XT:A:U/ {print}' in.sam > out.sam

Answer 1

[Wen.Huang]

bwa assigns non-unique reads a "0" mapping quality, if you filter by mapping quality by "samtools view -q 1", this gives you uniquely mapped reads.

[Abhi]

I think thats not true anymore. I see many reads which map to multiple location and have mapping quality in 10-23 range.

[Ric]

Thank you. Does non-unique reads mean that they match on different position equally good? But "1" mapping quality is different to what MarkDuplicates does? How to include in the above samtools command only paired-end (where both are unique)?