1 answer
First get a list of uniq scaffolds:
bgzip merge-test.vcf tabix merge-test.vcf.gz gzcat merge-test.vcf.gz | grep -v "^#" | cut -f1 | sort | uniq > scaff_names
Then Split by individual scaffolds:
parallel -a scaff_names "bcftools view merge-test.vcf.gz {} > {.}.vcf"
or by for loop:
for scaff in `cat scaff_names`; do bcftools view merge-test.vcf.gz $scaff > $scaff.vcf; done
For time being, you could use the 'for' loop option. You need to install GNU-Parallel. Its a wonderful tool.
hai again,
here is the few lines of output, missing headers in the vcf file.
##source_20150622.1=vcf-annotate(r953) -f Q=30
##contig=<ID=scaffold1>
##contig=<ID=scaffold2>
##contig=<ID=scaffold3>
##contig=<ID=scaffold4>
##contig=<ID=scaffold5>
I need something which has all the headers for each scaffold some thing like this: please see below
scaffold1 382 . T A 298.864 PASS .
scaffold2 460 . C T 2781.98 PASS .
scaffold2 534 . C T 3079.93 PASS .
scaffold3 828 . C T 3168.21 PASS .
scaffold3 918 . G A 2002.13 PASS .
scaffold4 929 . C T 1802.47 PASS .
scaffold4 943 . G C 1848.41 PASS .
scaffold5 995 . G A 897.007 PASS .
that has to be split into individual vcf files that has only one scaffold with variant information in each file. sorry if I haven't made it clear.
Run it on this file and let me know the problem you face. I could not understand from your data.
•
written
by
GouthamAtla
Hi Goutham,
Again looking for your help, I finally managed to split my large vcf file, with below script (from forums)
cut -f1 assm_1kb.fasta.fai | xargs -i mkfifo {}
cut -f1 assm_1kb.fasta.fai | xargs -i echo cat {} \| gzip \> {}.gz \&|sh
zcat fil-Q25-d10-QUAL30-PASS2.vcf.gz | awk '!/^#/{print>$1}'
The problem now is missing header for each scaffold, I managed to split the header with
head -n 60 fil-Q25-d10-QUAL30-PASS2.vcf | grep "^#" >header
Could you please help me with how to add the header information to each scaffold. please let me know if I am not clear.
Thank you
If you are looking for very simplistic approach, I would do something like this:
grep -v "^#" input.vcf | cut -f1 | sort | uniq > scaff_names
grep "^#" input.vcf > vcf_header
while read line
do
grep -v "^#" input.vcf | awk -v scaff=$line '{ if ( $1==scaff ) print }' | cat vcf_header - > $line.vcf
done < scaff_names
This should also split VCF by chromosome/scaffold with header intact. Hope this helps.
•
written
by
GouthamAtla
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