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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
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Is <INV> the inversions I needed in output VCF file? #313

Open Yiguan opened 4 years ago

Yiguan commented 4 years ago

Hi:

I am using lumpy to investigate inversion in pool-seq pair-end data, and I want to have inversion regions. After running lumpyexpress , I got an VCF output file. Are the positions breaking points in the vcf files? For example:

grep "<INV>" CWL21_1.fq.gz.vcf | awk '{split($8,aa,";");print $1,$2,aa[3],aa[4]}'

# output
ScA8VGg_76 1008001 SVLEN=168532 END=1176533
ScA8VGg_76 1402700 SVLEN=80 END=1402780
ScA8VGg_76 2391413 SVLEN=87 END=2391500
ScA8VGg_76 3066040 SVLEN=311 END=3066351

Does that mean I have four inversions on ScA8VGg_76? The first inversion starts from 1008001 and ends at 1176533?

Thanks!

ryanlayer commented 4 years ago

Seems so. Check the strands on these calls, you should have a mix of -- and ++ paired-end reads.

On Wed, Sep 4, 2019 at 11:11 PM Yiguan notifications@github.com wrote:

Hi:

I am using lumpy to investigate inversion in pool-seq pair-end data, and I want to have inversion regions. After running lumpyexpress , I got an VCF output file. Are the positions breaking points in the vcf files? For example:

grep "" CWL21_1.fq.gz.vcf | awk '{split($8,aa,";");print $1,$2,aa[3],aa[4]}'

output

ScA8VGg_76 1008001 SVLEN=168532 END=1176533 ScA8VGg_76 1402700 SVLEN=80 END=1402780 ScA8VGg_76 2391413 SVLEN=87 END=2391500 ScA8VGg_76 3066040 SVLEN=311 END=3066351

Does that mean I have four inversions on ScA8VGg_76? The first inversion starts from 1008001 and ends at 1176533?

Thanks!

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