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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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vcf2table output files problem #142

Closed motutaj closed 4 years ago

motutaj commented 4 years ago

Hello,

I have vcf files that were annotated with VEP, but instead of INFO[CSQ] I have:

INFO=<ID=ANN,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA

_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|SIFT|HGVS_OFFSET|HGVSg">

When I run java -jar /dist/vcf2table.jar file.vcf it works fine with output to stdout, but when i want to save it in txt file text is scrambled:

java -jar /dist/vcf2table.jar file1.vcf -o file1.txt [WARN][SnpEffPredictionParser]no INFO[EFF] or no description. This VCF was probably NOT annotated with SnpEff (old version). But it's not a problem if this tool doesn't need to access SnpEff Anotations. [WARN][VepPredictionParser]NO INFO[CSQ] found in header. This VCF was probably NOT annotated with VEP. But it's not a problem if this tool doesn't need to access VEP Annotations. vcf2table_out

lindenb commented 4 years ago

I don't have any color when I use a similar command. I suspect you also added the option --colors.

motutaj commented 4 years ago

I used with --colors and without --colors option and it didn't make difference.

Thank you, Monika

lindenb commented 4 years ago

on my side:

image

motutaj commented 4 years ago

no --colors

vcf2table_out

lindenb commented 4 years ago

sorry, I still don't get the same result:

image

motutaj commented 4 years ago

I figured it out. When I bgzip vcf file it worked correctly. Thanks for fast replies.

Monika