Sniffles

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Dear author, I am trying to phase SVs with HP added BAM files. The command I use is ```sniffles --phase```, other parameters are just default. In the output, I found...

jiadong324

install sniffles2 issues

6

I try to install sniffles2 using different strategies, but all failed: 1. pip install sniffles, see error: WARNING: pip is being invoked by an old script wrapper. This will fail...

guandailu

query about --minsvlen parameter

2

Hi, On using --minsvlen 50 as one of the parameters in multisample (trio) SV calling, I am still getting SVs which are upto 45 bp in length (both INS and...

prasundutta87

About output files

2

Hi, I had a questions about INS annotations in the output vcf file, as shown below:  The same as the insertion type, why the first line did not give...

linshengnan09

avoid reporting None as coverage, use -1 instead

1

wdecoster

"None" value in COVERAGE leads to an error with pyvcf

4

There are cases where Sniffles2 reports some of the "COVERAGE" field as "None" (e.g. "None,None,100,None,None"). As a result, reading a Sniffles2 VCF file using pyvcf throws the following error: ValueError:...

andyjslee

how sniffles2 merges SVs cross multiple samples

1

Hi Fritz, I tried sniffles2 to call SV using the Multi-Sample SV Calling mode, and I'd like to know how sniffles combines calling using multiple .snf files into a single...

Gongjiao94

Error when reading SNF header from files

1

Dear Fritz Sedlazeck, I am trying to run the Multi-sample calling with Sniffles v2.0.2 and I get an error in the second step. I run it like this: sniffles --minsupport...

mpalmada

Common parameters still relevant in multi-sample mode

3

Hi, From the `--help` page I've deduced that Sniffles categorizes its parameters in a few categories - Common parameters - SV Filtering parameters - SV Clustering parameters - Multi-Sample Calling...

eliavw

Research organism: bufo; Scaffolds of reference genome: 11 chromosomes and more than 700 unplaced contigs; Each sample bam file is split into three parts because sniffles run with error when...

maxineliu