How to rewrite convert2bed function from BEDOps using GNU parallel for batch processing?
How to rewrite convert2bed function from BEDOps using GNU parallel for batch processing?
Here is the code I have tried (not working (it can`t see the input):
parallel './convert2bed --input=vcf < {} > {.}.converted_BED.bed' :::*.vcf
However, it works without GNU parallel:
./convert2bed --input=vcf < SRR5152948_filter.recode.vcf > SRR5152952_converted_BED.bed
Need help how to apply GNU parallel engine correctly.
Thx.
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jean.elbers
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texaswhiskey1969 •
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texaswhiskey1969 •
1 answer
ls *.vcf > samples
parallel './convert2bed --input=vcf < {} > {}.converted_BED.bed' <samples
Note: Not tested with bedops
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You might use the
bam2bed_gnuParallelhelper script as a basis for something that is tested: https://github.com/bedops/bedops/blob/master/applications/bed/conversion/src/wrappers/bam2bed_gnuParallel