Hi, I am trying to use BECOPS vcf2bed argument to convert a 19G vcf file to a bed file. However, it only partially converted the file to a bed format. I tried using a smaller 456kb ssr marker vcf file and it also was partially processed. I have also tried using the "--max-mem" flag and the outcome remained the same. Does anyone have an idea as to why this is occurring?
Thank you
T
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trevishuggins316 •
It is possible that your /tmp folder is filling up with intermediate data during the sorting step. Some /tmp or swap folders are not large enough to hold intermediate results.
Use --sort-tmpdir <dir> with vcf2bed to specify an alternative directory <dir> that can contain more than 19GB of data (a worst-case scenario: where all variants are on one chromosome).
Alternatively, use --do-not-sort with vcf2bed to keep the result unsorted, and then sort afterwards with sort-bed --tmpdir <dir>.
Thank you.
I used the alternative approach and it worked. Again, Thank you for your assistance.
Regards,
T
Did the first approach not work? (If there is a bug I’d like to fix it, if I can.)
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