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