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Hi Brent and Dave, Not sure if this question is more appropriate here or under svtools. I have been jointly calling SVs in families with Lumpy. Is there a command...

andrewSharo

The time and Mem needed to run speedseq SV

3

Hi, When I used over 1000 samples to run speedseq SV, the running time varied from 2h to 36h. It turned out that those sv.vcf.gz files which needed more than...

sususy

Missing Sample Names in lmerge file

2

Hello. I was able to successfully generate a merged vcf for a large number of accessions. However, of over 27,000 SV calls there were 128 calls that did not have...

egoetz

svtools Genotype + Key Error: 'END'

1

I have used the svtools protocol at https://github.com/hall-lab/svtools/blob/master/Tutorial.md . However, i am having the below error while using svtools genotype: Running svtyper with options: /svtools/bin/svtyper/svtyper --split_weight 1 -n 1000000 --disc_weight...

arumds

This has come up a couple of times in interactions with folks using the tools. Make sure that the tutorial mentions using the exclude files and includes links to the...

ernfrid

Definitely upon early exit it doesn't. Ensure that it does in both clean and unclean exits.

ernfrid

change prune default to think the file is sorted

1

This is more memory efficient for big cohorts, but will need to add a check to detect when users pass in an unsorted file.

ernfrid

@abelhj reports this would be a nice feature to have.

ernfrid

For speed, no checking is done currently, but that means it is possible to paste together files that have different sort orders. Even an optional check that sort order is...

ernfrid

BND Variants on GL contigs move during file conversion

1

For example, ``` $ cat roundtrip_diff.out | cut -f1-4 | less 4a5 > ##INFO= 81118,81119c81119,81120 < GL000193.1 16 13312_2 N < GL000193.1 25 13311_2 N --- > GL000193.1 17 13312_2...

ernfrid