SnpSift split outputs only the first chromosome

[kmavrommatis]

Hi, I have a 3.8Gb VCF file produced by a WGS pipeline mapping on hg38 and mutation calling using Mutect2. The file contains chromosomes chr1 ... chr22, chrX, chrY and chrM in that order.

Running java -jar SnpSift.jar split $PWD/sample.mnv.hg38.vcf.gz

produces a single file named

sample.mnv.hg38.chr1.vcf which contains only the first few hundreds of positions in chr1 and exists without any error

I have not managed to replicate the error with a smaller size vcf file but happy to share the full vcf file if necessary.

Thanks in advance for any advise/help

[emyli14]

I have a similar problem, though my VCF is 1TB, mapped to hg19, processed with GATK and also includes GL contigs. The sample.1.vcf output file contains ~8,500 variants and in total there are ~42,000,000 variants in the original VCF. Same result if trying the -l option to split every N lines.

[alejandrogzi]

I am having the exact same issue. Did you find any solution?

[blueivy1117]

I have the same issue, output only 124M of data and stopped without any error or output in the log (run on the cluster).

[yhkithub]

I am having the exact same issue. Did you find any solution?

[dianacornejo]

@kmavrommatis any idea why split does not work? It does not give any error either when trying to split a vcf files using the -l argument.

[alkaZeltser]

I too have had the same problem!