Anne Marie Noronha

merging svaba

2

i was unable to merge SvABA calls using SURVIVOR and I don't see any issues regarding SvABA, so this might be a new topic for this tool. My command is:...

start, end and length not adding up

5

i am testing annotsv and finding that the first few columns in certain examples do not make sense and I was hoping it could be clarified. i have the following...

feature request: ignore duplicate-marked reads

1

this issue is to request ignoring dup reads as an option. gatk best practice is to keep all duplicates in the bam, and i have read from a few issues...

We are reaching out to understand any major differences between svaba and snowman, that could cause the calls to be very different. We recently downloaded some PCAWG results that were...

how to retain INFO columns in maf2vcf?

1

i have recently tested out maf2vcf.pl: ``` perl /opt/maf2vcf.pl \\ --input-maf ${inputMaf} \\ --ref-fasta ${genomeFile} \\ --output-vcf test.vcf \\ --output-dir test ``` And I found that all my annotations were...

bedpetovcf does not work with vcftobedpe output as input

1

I'm trying the dockerhub image with svtools and running as follows: ``` singularity exec -e --no-home docker://halllab/svtools:v0.5.1 svtools vcftobedpe -i $inputvcf -o vcftobedpe.bedpe -t tmp singularity exec -e --no-home docker://halllab/svtools:v0.5.1...

i have the following vcf record that i believe is not correctly represented in the result when using vcftobedpe: ``` 6 57184412 Pipeline_TRA_6_57184412 N N]8:36752983] . PASS END=36752983;Callers=manta,delly;NumCallers=2;CHR2=8;SVTYPE=TRA;STRANDS=++;delly_CIEND=-2,2;delly_CIPOS=-2,2;delly_PE=3;delly_MAPQ=60;delly_SRMAPQ=60;delly_SR=12;delly_SRQ=0.985981;delly_CE=1.93075;delly_CT=3to3;delly_PRECISE;delly_SVMETHOD=EMBL.DELLYv0.8.2;delly_INSLEN=0;delly_HOMLEN=2;delly_RDRATIO=1.17045;delly_SOMATIC;manta_CIPOS=0,1;manta_MATEID=MantaBND:136490:1:6:0:0:0:1;manta_HOMLEN=1;manta_HOMSEQ=A;manta_BND_DEPTH=70;manta_MATE_BND_DEPTH=96;manta_SOMATIC;manta_SOMATICSCORE=90;NumCallersPass=2 delly_GQ:delly_FT:delly_RC:delly_RCL:delly_RCR:delly_CN:delly_DR:delly_DV:delly_RR:delly_RV:manta_PR:manta_SR 10000:PASS:117:50:63:2:36:3:28:16:44,3:55,16...

pip install fails

2

We are trying to install `svtools` in a docker container using `pip install svtools`. Our docker already has `Python 2.7.13` installed on it. The error we get is quite long...

I am having issues understanding the columns for SV inputs. It seems like `Tumor_Varcount` is the number of reads supporting the ALT in the tumor sample, and `Tumor_Depth` seems like...

Error running deconvolution_fit_SV with plotting

5

Using the example script with the example Rdata gives me the following error: ``` Error in RCircos.Validate.Genomic.Data(genomic.data, "link", genomic.columns) : One or more genomic position in plot data is outside...