svaba

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Challenge of running svaba with FFPE tumor/normal pairs

1

Svaba is awesome! For frozen WGS samples, we got a genome done within 4-5 hours with low CPU/memory footage. However, as we run tumor-normal pairs on FFPE samples,it is taking...

ipstone

Hi Jeremiah, Thanks for your great work! Svaba is awesome! I wonder if there is any plan to replace bwa-mem with minimap2 which is compatible with paired end short reads...

alartin

Query regarding SV calls

2

Hello, I ran svaba on few BAM files (similar samples) . I observed that a SV call is made in some samples and not in others, even though the discordant...

pwanj

calculate SR DR through alignment file

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Hi, This is the alignment information for a somatic SV event. ``` Global BP: : 1:1,038,901(-) to 1:1,039,297(+) SPAN 396 c_1_1029001_1054001_367C n001:0 t000:6 ins_aginst_contig 0 del_against_contig 0 c_1_1029001_1054001_367C >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>................................................................................................................ C[0,1...

thelingxichen

Are there any materials that explain how LO works? I want to do some filtering by LO and I'm not sure what threshold I should put my filter at. Thanks,...

yoyosef

Example BAM file and output file are available?

2

Hi Jeremiah, I wonder if you provide example BAM files and output file (.vcf) that I can test svaba and replicate the result. It is because I like to test...

biotech25

Hi, I downloaded tumor and normal BAM files of ICGC donor ID, "DO48701" from ICGC. The tumor BAM file ID is FI44968, and normal BAM file ID is FI44967. I...

biotech25

Somatic rearrangement scores: `LO` or `SL`

4

Hi Jeremiah, I have a question about the scores for somatic rearrangements. I was checking the detected variants in "*.svaba.somatic.sv.vcf" and was wondering whether "LO" in the FORMAT column is...

jnktsj

Problem with long deletion

6

Hi Walaj, I tried to use SvABA on long deletion range from 1mbp to 150mbp in simulated bam file. SvABA works well when only small indel are included. However, when...

VicBioDev

svaba segmentation fault (core dumped)

11

Hi, When I used svaba to run in germline mode, with the following command: ~/tools/svaba run -t ../../../2.bam -k k.bed -a RT -L 6 -I -p 10 -G ssc11_1.fa the...

yungruifei