Bcftools view error
1
0
Entering edit mode
8 months ago
yvyu • 0

Hello, I have been running into this error.

[E::bgzf_uncompress] Inflate operation failed: 1
Error: BCF read error

I am trying to create bcf files from vcf.gz, but it keeps running into this error. Does this mean my vcf.gz files are corrupted?

bcftools • 849 views
ADD COMMENT
1
Entering edit mode

first show us the output of

gunzip -t the.vcf.gz

also, show us the bcftools command line.

ADD REPLY
0
Entering edit mode

The bcftools command line is as follows:

The output of gunzip is as follows (which I am assuming means that there is some issue with the downloading of this file):

gzip: 1kGP_high_coverage_Illumina.chr1.filtered.SNV_INDEL_SV_phased_panel.vcf.gz: invalid compressed data--crc error

gzip: 1kGP_high_coverage_Illumina.chr1.filtered.SNV_INDEL_SV_phased_panel.vcf.gz: invalid compressed data--length error
ADD REPLY
0
Entering edit mode

The output of gunzip is as follows (which I am assuming means that there is some issue with the downloading of this file):

your files are broken

ADD REPLY
1
Entering edit mode

furthermore, you have to comment (+validate?) the answer you got: 1000G Reference Panel Hg38 Michigan Imputation Server

ADD REPLY
0
Entering edit mode
8 months ago

The output of gunzip is as follows (which I am assuming means that there is some issue with the downloading of this file):

your files are corrupted/broken or not gzip compressed.

Download them again.

ADD COMMENT
0
Entering edit mode

Okay, thank you. I will try that.

ADD REPLY

Login before adding your answer.

Traffic: 1479 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6