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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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No split read support found #261

Open thelingxichen opened 6 years ago

thelingxichen commented 6 years ago

Hi,

After running traditional lumpy on normal and tumor reads seperately, I found all split read support (SR) are 0. Is this acceptable?

I haven't do svtyper yet.

Thanks.

ryanlayer commented 6 years ago

How did you extract split reads?

On Aug 2, 2018, at 2:35 AM, Paprika Chan notifications@github.com wrote:

Hi,

After running traditional lumpy on normal and tumor reads seperately, I found all split read support (SR) are 0. Is this acceptable?

I haven't do svtyper yet.

Thanks.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

thelingxichen commented 6 years ago

The commands is:

samtools view -h /home/xuchang/mnt/dl380/FS_PROJECTS/WHOC/Bwa/merge_bam/OC001B/OC001B.bam | /home/BIOINFO_TOOLS/mutation_tools/LUMPY/lumpy-sv/scripts/extractSplitReads_BwaMem -i stdin | /home/BIOINFO_TOOLS/mutation_tools/SamTools/SamTools-1.3/bin/samtools view -Sb - > OC001B.splitters.unsorted.bam
samtools sort OC001B.splitters.unsorted.bam -o OC001B.splitters.bam
ryanlayer commented 6 years ago

How big are your splitter and discordsnt bams?

On Aug 2, 2018, at 10:46 PM, Paprika Chan notifications@github.com wrote:

The commands is:

samtools view -h /home/xuchang/mnt/dl380/FS_PROJECTS/WHOC/Bwa/merge_bam/OC001B/OC001B.bam | /home/BIOINFO_TOOLS/mutation_tools/LUMPY/lumpy-sv/scripts/extractSplitReads_BwaMem -i stdin | /home/BIOINFO_TOOLS/mutation_tools/SamTools/SamTools-1.3/bin/samtools view -Sb - > OC001B.splitters.unsorted.bam samtools sort OC001B.splitters.unsorted.bam -o OC001B.splitters.bam — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.