samblaster

[woodoo46]

Hi Lumpy Developers,

When extracting splitted reads and disconcordant reads, do we really need to use samblaster? What will happen if we do not use samblaster?

Thanks.

George

[ryanlayer]

There are other ways to extract discordant and split reads, and you have a preferred one I suggest you use it.

Ryan

On Sep 29, 2017, at 1:27 PM, woodoo46 notifications@github.com wrote:

Hi Lumpy Developers,

When extracting splitted reads and disconcordant reads, do we really need to use samblaster? What will happen if we do not use samblaster?

Thanks.

George

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[woodoo46]

We have already bwa generated bam file, can we just use the the following commands to extract diconcordant reads and split reads?

For split reads: ${samtools} view -h ${inbam} | \ ${extract_splitters} -i stdin | \ ${samtools} view -Sb - > ${tempbam}

For disconcordant reads: ${samtools} view -b -F 1294 ${inbam} > ${tempbam}

In other words, if we skip samblaster, the reads extracted are still good for Lumpy?

Thanks.

George

[ryanlayer]

I think so. You can also try the beta version we have in lumpy-sv called lumpy_filter. It should be faster.

On Sun, Oct 1, 2017 at 6:35 AM, woodoo46 notifications@github.com wrote:

We have already bwa generated bam file, can we just use the the following commands to extract diconcordant reads and split reads?

For split reads: ${samtools} view -h ${inbam} | ${extract_splitters} -i stdin | ${samtools} view -Sb - > ${tempbam}

For disconcordant reads: ${samtools} view -b -F 1294 ${inbam} > ${tempbam}

In other words, if we skip samblaster, the reads extracted are still good for Lumpy?

Thanks.

George

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-- Ryan Layer