It should be a text file with each VCF filepath on a separate line. here's an example showing merging in batches of 200 samples, and finally into a VCF of the whole cohort

pwd
# /gscmnt/gc2719/halllab/users/cchiang/dev/vcf_paste_2016-01-04

wc -l /gscmnt/gc2802/halllab/sv_aggregate/merge/re-GT/all.cn.txt
# 4907 /gscmnt/gc2802/halllab/sv_aggregate/merge/re-GT/all.cn.txt

mkdir -p split
split -a 2 -d -l 200 /gscmnt/gc2802/halllab/sv_aggregate/merge/re-GT/all.cn.txt split/spl

# 2 hour 2 min
# commit (svtyper): 2b24a61503eab8274d659e70da357030614c9727
for FILE in `ls split`
do
    bomb -m 8 "/gscmnt/gc2719/halllab/users/cchiang/src/svtyper/scripts/vcf_paste.py -q -f split/$FILE | gzip -c > $FILE.vcf.gz"
done

ls spl*.vcf.gz > batch_paste.txt

bomb -m 1 "/gscmnt/gc2719/halllab/users/cchiang/src/svtyper/scripts/vcf_paste.py -q -f batch_paste.txt | bgzip -c > final.vcf.gz"

from svtools.

Ah. So -f expects a FILE of files, not a list of files (as the usage
states).

On Fri, Feb 12, 2016 at 11:15 AM, Colby Chiang [email protected]
wrote:

should work with each VCF filepath on a separate line. here's an example
showing merging in batches of 200 samples, and finally into a VCF of the
whole cohort

pwd# /gscmnt/gc2719/halllab/users/cchiang/dev/vcf_paste_2016-01-04

wc -l /gscmnt/gc2802/halllab/sv_aggregate/merge/re-GT/all.cn.txt# 4907 /gscmnt/gc2802/halllab/sv_aggregate/merge/re-GT/all.cn.txt

mkdir -p split
split -a 2 -d -l 200 /gscmnt/gc2802/halllab/sv_aggregate/merge/re-GT/all.cn.txt split/spl

2 hour 2 min# commit (svtyper): 2b24a61503eab8274d659e70da357030614c9727for FILE in ls splitdo

bomb -m 8 "/gscmnt/gc2719/halllab/users/cchiang/src/svtyper/scripts/vcf_paste.py -q -f split/$FILE | gzip -c > $FILE.vcf.gz"done

ls spl*.vcf.gz > batch_paste.txt

bomb -m 1 "/gscmnt/gc2719/halllab/users/cchiang/src/svtyper/scripts/vcf_paste.py -q -f batch_paste.txt | bgzip -c > final.vcf.gz"

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#44 (comment).

Ryan Layer

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This seems to work too:

svtools vcfpaste -f <(ls *vcf)

On Fri, Feb 12, 2016 at 11:39 AM, Ryan Layer [email protected] wrote:

Ah. So -f expects a FILE of files, not a list of files (as the usage
states).

On Fri, Feb 12, 2016 at 11:15 AM, Colby Chiang [email protected]
wrote:

should work with each VCF filepath on a separate line. here's an example
showing merging in batches of 200 samples, and finally into a VCF of the
whole cohort

pwd# /gscmnt/gc2719/halllab/users/cchiang/dev/vcf_paste_2016-01-04

wc -l /gscmnt/gc2802/halllab/sv_aggregate/merge/re-GT/all.cn.txt# 4907 /gscmnt/gc2802/halllab/sv_aggregate/merge/re-GT/all.cn.txt

mkdir -p split
split -a 2 -d -l 200 /gscmnt/gc2802/halllab/sv_aggregate/merge/re-GT/all.cn.txt split/spl

2 hour 2 min# commit (svtyper): 2b24a61503eab8274d659e70da357030614c9727for FILE in ls splitdo

bomb -m 8 "/gscmnt/gc2719/halllab/users/cchiang/src/svtyper/scripts/vcf_paste.py -q -f split/$FILE | gzip -c > $FILE.vcf.gz"done

ls spl*.vcf.gz > batch_paste.txt

bomb -m 1 "/gscmnt/gc2719/halllab/users/cchiang/src/svtyper/scripts/vcf_paste.py -q -f batch_paste.txt | bgzip -c > final.vcf.gz"

—
Reply to this email directly or view it on GitHub
#44 (comment).

Ryan Layer

Ryan Layer

from svtools.

i'm actually just going to reopen this so we remember to clarify the usage

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