Entering edit mode
5.3 years ago
9521ljh
▴
50
i have a bed file
cat AMP_region.bed
chr1 157543538 157567870
chr1 160313062 160328742
chr1 163291722 163325553
chr2 85360582 85537511
samtools depth -a -b AMP_region.bed test.bam
above command no output anything. what is wrong?
i already tried removing prefix 'chr', but empty output...
samtools depth -a -r 1:50246462-59249785 test.bam
1 50246462 69
1 50246463 69
1 50246464 69
it is work well
Thus i think bed file is something wrong..
There you already have your answer. The
chr
prefix must be removed. Please show how you removed it in the first place (command line).i followed this command line:
This also output empty