there is no SR support

[arkyl]

Hi, The lumpy result for my input bam didn't have SR support, i.e. all are SR=0. The bam did have the SA tag. I am wondering what might be the issue. Thanks a lot!

The lumpy command line is : lumpyexpress -B input.bam -o lumpy.vcf -x exclude_bed

Yue

[ryanlayer]

How were the samples aligned?

On Wed, Oct 3, 2018 at 11:20 AM ylark notifications@github.com wrote:

Hi, The lumpy result for my input bam didn't have SR support, i.e. all are SR=0. The bam did have the SA tag. I am wondering what might be the issue. Thanks a lot!

The lumpy command line is : lumpyexpress -B input.bam -o lumpy.vcf -x exclude_bed

Yue

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[arkyl]

it was aligned by Sentieon pipeline, which used bwa mem aligner and then a gatk like postprocess (mark duplicate, realign indel).

an example line: A00364:9:H3MWMDSXX:2:2551:7229:29606 355 chr1 1577876 60 42M108H chr13 103355267 0 GCCAGTTCTGGGTGGAGTCTGCCGTCCAGAATGAGATTTATG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:0 MD:Z:42 AS:i:42 XS:i:22 RG:Z:NA12878_S10_001_1 SA:Z:chr13,103355244,+,42S108M,60,0;

Thanks.

[ryanlayer]

Does your splitter file have anything in it?

On Wed, Oct 3, 2018 at 1:43 PM ylark notifications@github.com wrote:

it was aligned by Sentieon pipeline, which used bwa mem aligner and then a gatk like postprocess (mark duplicate, realign indel).

an example line: A00364:9:H3MWMDSXX:2:2551:7229:29606 355 chr1 1577876 60 42M108H chr13 103355267 0 GCCAGTTCTGGGTGGAGTCTGCCGTCCAGAATGAGATTTATG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:0 MD:Z:42 AS:i:42 XS:i:22 RG:Z:NA12878_S10_001_1 SA:Z:chr13,103355244,+,42S108M,60,0;

Thanks.

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[arkyl]

I used lumpyexpress: lumpyexpress -B input.bam -o lumpy.vcf -x exclude_bed

And I didn't see intermediate files.

[ryanlayer]

Pass "-k" to keep the temp files, from there we can dig in.

On Wed, Oct 3, 2018 at 2:16 PM ylark notifications@github.com wrote:

I used lumpyexpress: lumpyexpress -B input.bam -o lumpy.vcf -x exclude_bed

And I didn't see intermediate files.

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[arkyl]

Hi Ryan, I used the -k parameter in lumpyexpress. But the output is only the final vcf. It didn't seem to keep the temp files.

~/software_installed/lumpy-sv/scripts/lumpyexpress -B ../NA12878_S10_R1_001.bam.chr22.bam -o NA12878_S10_R1_001.bam.chr22.bam.dash-k.vcf -k &

Thank, Yue

[ryanlayer]

That is strange. Why don't you give https://github.com/brentp/smoove a try. We have made many fixes to the extraction process that should help.

On Fri, Oct 5, 2018 at 9:00 AM ylark notifications@github.com wrote:

Hi Ryan, I used the -k parameter in lumpyexpress. But the output is only the final vcf. It didn't seem to keep the temp files.

~/software_installed/lumpy-sv/scripts/lumpyexpress -B ../NA12878_S10_R1_001.bam.chr22.bam -o NA12878_S10_R1_001.bam.chr22.bam.dash-k.vcf -k &

Thank, Yue

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[arkyl]

Thanks much. I will try smoove.