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For all other contigs, comparable code gives all reads that are mapped to that contig, whereas for chrY, this returned a suspiciously large bam file (larger than the chrX file). I checked through temp.chrY.bam and all of the unmapped reads from my bam were present in this file, that is, every read that is sliced out using
Hi,
Have been using sambamba for a couple of days. I split up a human genome bam file (header at the bottom of the note) using the code
sambamba_v0.4.6 slice
-o temp.chrY.bam
.bam
'chrY'
For all other contigs, comparable code gives all reads that are mapped to that contig, whereas for chrY, this returned a suspiciously large bam file (larger than the chrX file). I checked through temp.chrY.bam and all of the unmapped reads from my bam were present in this file, that is, every read that is sliced out using
sambamba_v0.4.6 slice
-o temp.unmapped.bam
.bam
'*'
is also present in the chrY file.
I was wondering whether this might be a bug related to chrY being the final contig in my bam file and can provide an example sam file if required
All the best, sambamba is a fine tool and I'm sure I can work around the problem.
Russ,
U. Liverpool
@hd VN:1.3 SO:queryname
@sq SN:chr1 LN:249250621
@sq SN:chr2 LN:243199373
@sq SN:chr3 LN:198022430
@sq SN:chr4 LN:191154276
@sq SN:chr5 LN:180915260
@sq SN:chr6 LN:171115067
@sq SN:chr7 LN:159138663
@sq SN:chr8 LN:146364022
@sq SN:chr9 LN:141213431
@sq SN:chr10 LN:135534747
@sq SN:chr11 LN:135006516
@sq SN:chr12 LN:133851895
@sq SN:chr13 LN:115169878
@sq SN:chr14 LN:107349540
@sq SN:chr15 LN:102531392
@sq SN:chr16 LN:90354753
@sq SN:chr17 LN:81195210
@sq SN:chr18 LN:78077248
@sq SN:chr19 LN:59128983
@sq SN:chr20 LN:63025520
@sq SN:chr21 LN:48129895
@sq SN:chr22 LN:51304566
@sq SN:chrX LN:155270560
@sq SN:chrY LN:59373566
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