Why samtools depth error
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3.1 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..

sequence gene sequencing • 709 views
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There you already have your answer. The chr prefix must be removed. Please show how you removed it in the first place (command line).

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i followed this command line:

sed 's/chr//' AMP_region.bed

cat AMP_region.bed
1    157543538       157567870
1    160313062       160328742
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This also output empty

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3.1 years ago
9521ljh ▴ 50

sorry, i solve this problem...

actually test.bam file is another directory. Thus i copy it in same directory ( bed, bam, bai)

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