jasonbhn

Hi, I'm running paragraph on 1 sample and it returned this error: ``` [E::cram_itr_query] Query with tid=-1 not implemented for CRAM files Aborted (core dumped) ``` What does this mean?...

Hi, I was trying to modify [sv-pipeline](https://github.com/hall-lab/sv-pipeline/blob/master/scripts/Post_Merge_SV.wdl) to be able to classify variant calls of a smaller cohort. calc_params would fail if deletions are not present in the naive Bayes...

vcftobedpe complains about no END field in LUMPY BNDs.

1

Hi In version 0.5.1, I did `svtools vcftobedpe -i gtex.lumpy.gs.melt.high_conf_MAF0.01.vcf -o gtex.lumpy.gs.melt.high_conf_MAF0.01.bedpe` to convert vcf to bedpe files however the error: `ValueError: END entry in VCF required for conversion to...

Hi Fritz, I'm analyzing a set of SURVIVOR merged SVs called using MANTA. There are many INS with POS!=END, which baffles me as I recall INS should just be the...

hi! thank you for developing this neat package. Do you have any plans to implement some way to select the optimal numbers of PCs based on various methods such as:...

allow_intrasample throws exceptions

1

hi Melanie, I'm trying to combine multiple caller's SV calls into 1 vcf, the --allow_intrasample option seems like the natural way to go. but i've been running into this exception...

Need clearer instructions on each parameter for GATK-SV-single-sample

2

Hi, I'm trying to use the workspace help-gatk/GATK-Structural-Variants-Single-Sample](https://anvil.terra.bio/#workspaces/help-gatk/GATK-Structural-Variants-Single-Sample to call SVs on a few individuals I have. I decided to use the 1000G reference panel on https://console.cloud.google.com/storage/browser/gatk-sv-resources-public?authuser=0 but this still...