vcf2bed argument in bedops partially process vcf file

Question

[trevishuggins316]

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

Answer 1

[Alex Reynolds]

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>.

[trevishuggins316]

Thank you.

I used the alternative approach and it worked. Again, Thank you for your assistance.

Regards,

T

[Alex Reynolds]

Did the first approach not work? (If there is a bug I’d like to fix it, if I can.)