Potential bug with bedtools intersect

[Miikka Voutilainen]

Hey,

I was using bedtools v2.30.0. I intersected a bam file with coordinate bed (SNP list).

I noticed, that when using -bed flag, the mapq values in output were incorrect. I got no entries with mapq value over 30. However, when using bam output (so without -bed flag) there were alignments with mapq > 30. I tested this also using samtools software (http://www.htslib.org/doc/samtools-view.html) with bedtools intersect generated bam file.

Command:

bedtools intersect -abam  input.bam -b SNPs.bed -wa -bed -v > output.bed

Expected output:

Bed-file with correct MAPQ values.

True output:

Bed-file with incorrect MAPQ values.

Best Regards,

Miikka

[Aaron Quinlan]

Hi Mikka,

Could please show an example of the SAM records with MAPQ>30 and the resulting output from bedtools for the same records?  Even a few such lines of output should suffice.

Aaron

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