Comments (2)
Sure it does, at least if the input BED file also contains a "name" field in the 4th column.
$ more some-targets.bed
chr1 30330 30540 MIR1302-10
chr1 35051 35290 FAM138A
chr1 35290 35529 FAM138A
chr1 35623 35833 FAM138A
chr1 69039 69294 OR4F5
chr1 69294 69549 OR4F5
chr1 69549 69804 OR4F5
chr1 69804 70059 OR4F5
chr1 367618 367873 OR4F16
chr1 367873 368128 OR4F16
$ samtools bedcov -Q 1 some-targets.bed some-reads.bam
chr1 30330 30540 MIR1302-10 0
chr1 35051 35290 FAM138A 0
chr1 35290 35529 FAM138A 50
chr1 35623 35833 FAM138A 0
chr1 69039 69294 OR4F5 0
chr1 69294 69549 OR4F5 1228
chr1 69549 69804 OR4F5 748
chr1 69804 70059 OR4F5 0
chr1 367618 367873 OR4F16 0
chr1 367873 368128 OR4F16 0
$ samtools
Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.19-44428cd
...
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Ah I see, yeah my BED file was missing the 4th column. Thanks!
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