acontrerasg

methylDackel extract segmentation fault

1

Hello, I am trying to use the MethylDackel extract command with the default syntax: `MethylDackel extract ref.fa sorted_alignmnet.bam ` but I get a somewhat cryptic error: `Segmentation fault` However, with...

dear Hajk, I noticed that, under certain headers formats, in my case: >Chr1 >Chr2 >Chr3 >Chr4 >Chr5 >Chr6 >Chr7 >Scaffold_1 >Scaffold_2 >Scaffold_3 The tool chops out part of the genomic...

Parsing sample names as external variable are not recognized in the Sample field.

1

Given a multisample VCF file with different samples, if the sample name is given as a external variable, such as `sample_name="NA00001" ` ` zcat MULTI_VCF | vawk -v ext_var=$sample_name '{print...

custom genome and sex chromosome error

2

Hello, I am running this pipeline with the batch command and a custom genome that lacks sex chromosomes. The batch command lacks the option '-x' to specify to skip the...

Suggestion: Return TSD=None for easy parsing

1

Hello , First of all, thanks for developing the tool. I have been playing around with the VCF output file and I really like that it is very information rich....