Bcftools view error

Question

[yvyu]

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?

[Pierre Lindenbaum]

first show us the output of

gunzip -t the.vcf.gz

also, show us the bcftools command line.

[yvyu]

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

[Pierre Lindenbaum]

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

[Pierre Lindenbaum]

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

Answer 1

[Pierre Lindenbaum]

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.

[yvyu]

Okay, thank you. I will try that.