Question: [ti_index_core] the chromosome blocks not continuous at line xxxx, is the file sorted? [pos 1]
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gravatar for shubhra.bhattacharya
6 months ago by
shubhra.bhattacharya40 wrote:

While using tabix I encounter the following error.

[ti_index_core] the chromosome blocks not continuous at line 5891584, is the file sorted? [pos 1]

Command: /data/ngs/programs/tabix-0.2.6/tabix -p vcf SRR12954_1.fastq.gz_20180228112323.GRCH38.vcf.gz

I have zipped the vcf file using bgzip data/ngs/programs/tabix-0.2.6/bgzip -c SRR12954_1.fastq.gz_20180228112323.GRCH38.vcf > SRR12954_1.fastq.gz_20180228112323.GRCH38.vcf.gz

I have also sorted the vcf using vcf-sort but run into the same problem

index variant vcf • 471 views
ADD COMMENTlink written 6 months ago by shubhra.bhattacharya40

what is the context around the line 5891584 ?

gunzip -c SRR12954_1.fastq.gz_20180228112323.GRCH38.vcf.gz | cut -f 1,2,4,5 | nl | awk '(NR> 5891580 && NR< 5891590)'
ADD REPLYlink written 6 months ago by Pierre Lindenbaum112k

5891581 chrMT 16129 G A 5891582 chrMT 16129 G A 5891583 chrMT 16179 CAA C 5891584 chr1 3088286013 AAA CCC 5891585 chrMT 16182 A C 5891586 chrMT 16183 A C 5891587 chrMT 16186 C T 5891588 chrMT 16188 C T 5891589 chrMT 16189 T C

This is the output of the command. The chr1 is just dropping by in b/w the chrMT chromosome block.

ADD REPLYlink written 6 months ago by shubhra.bhattacharya40
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