Subsampling Bam File With Samtools

Question

[madbessoul]

Hi,

I am trying to subsample from a bam file using the samtools view -s command. This is working when sampling 50% or lower (-s 42.50, 42 being the seed), but anything higher fails (returns an empty file).

He are the exact commands I use

samtools view -s 0.25 -b chr6_all.bam > chr6_25p.sam #works
samtools view -s 0.50 -b chr6_all.bam > chr6_50p.sam #works
samtools view -s 0.75 -b chr6_all.bam > chr6_75p.sam #does not work

I also made sure that 49% is working, but 51% is not. Any ideas, suggestions, or is this an intended mechanic? There doesn't seem to be any documentation about the subsampling parameter in samtools docfile.

Thanks

[giulia.trauzzi]

Hi! This post was very useful to me. I am trying however to visualise my reduced bam file on IGV but an index is required. Is there a way to create a index for the bam file that is randomly subsampled with samtools -s ?

Thanks

Giulia

[ATpoint]

samtools index, nothing special here

[giulia.trauzzi]

Thank you very much

Answer 1

[John Marshall]

Subsampling not working for fractions above 50% is a known bug in samtools 0.1.18. (See [Samtools-help] Randomized Subsampling Bam File / Subsampling above 50%.)

The bug was fixed in March last year; samtools 0.1.19 contains the corrected version.

[madbessoul]

Thank you very much, updating to the lastest version right now.

[Dataman]

You could accept one of the answers as the final answer.

Answer 2

[14134125465346445]

I have also tried sambamba, and found it to be faster in multi-threaded mode compared to samtools 0.1.19

~/src/sambamba/sambamba_v0.3.3 view -h -t $numThreads -s $fractionOfReads -f bam --subsampling-seed=$seed $testBam -o $subsampledTestBam

[eidriangm]

When subsampling with samtools or sambamba do all the mappings (uniques, multiple and null) of a read are included in the new bam file?