Post date: Jun 23, 2020 1:7:59 PM
I need to find a way to filter the vcf file to retain only the individuals that have a >4 mean read depth.
Extract vector of names from vcf.
Install bcftools: use commmand -
Command:
bcftools view -s sample1,sample2 file.vcf > filtered.vcf
bcftools view -s potr-003-B,potr-003-S,potr-005-B,potr-005-S,potr-007-B,potr-007-S,potr-009-B,potr-009-S,potr-011-S,
potr-013-S,potr-015-B,potr-015-S,potr-017-B,potr-017-S,potr-019-S,potr-021-S,potr-022-S,potr-023-B,potr-023-S,potr-025-B,
potr-025-S,potr-027-B,potr-031-B,potr-031-S,potr-033-B,potr-033-S,potr-035-B,potr-035-S,potr-037-B-rep,potr-037-B-Rp,
potr-037-B,potr-039-S,potr-043-B,potr-045-S,potr-047-B,potr-049-S,potr-051-B,potr-051-S,potr-053-B,potr-053-S,
potr-055-S-Rp,potr-055-S,potr-059-S,potr-061-B,potr-063-S,potr-065-B,potr-065-S,potr-067-B,potr-067-S,potr-069-B,
potr-069-S,potr-071-B,potr-073-S,potr-075-B,potr-075-S,potr-079-B,potr-079-S,potr-081-B,potr-081-S,potr-083-S,
potr-085-B,potr-085-S,potr-086-S,potr-087-B,potr-087-S,potr-091-B,potr-091-S,potr-093-B,potr-093-S,potr-095-B,
potr-095-S,potr-099-B,potr-101-B,potr-101-S,potr-103-B,potr-103-S,potr-105-B,potr-107-B,potr-107-S,potr-111-B,
potr-113-B,potr-113-S,potr-115-S,potr-117-B,potr-117-S,potr-119-B,potr-121-B,potr-121-S,potr-123-B,potr-123-S,
potr-125-B,potr-129-B,potr-129-S-rep,potr-129-S-Rp,potr-129-S,potr-131-S,potr-133-B,potr-133-S,potr-135-S,potr-137-B,
potr-137-S,potr-139-B,potr-141-B,potr-143-S,potr-145-S,potr-147-S,potr-149-B,potr-149-S,potr-151-B,potr-151-S,potr-153-B,
potr-153-S,potr-155-B,potr-155-S,potr-157-B,potr-157-S,potr-159-B,potr-159-S,potr-163-B,potr-163-S,potr-165-B,potr-165-S,
potr-167-B,potr-167-S,potr-169-B,potr-169-S,potr-171-B,potr-171-S,potr-173-B,potr-173-S,potr-175-B,potr-175-S,potr-177-S,
potr-179-B,potr-179-S,potr-181-S,potr-183-B1,potr-183-B2,potr-183-S,potr-184-B,potr-185-B,potr-187-B,potr-191-S,
potr-195-B,potr-195-S,potr-197-B,potr-199-B,potr-199-S,potr-201-B,potr-201-S,potr-203-S,potr-205-S,potr-207-S,
potr-209-B,potr-211-B,potr-211-S,potr-213-B,potr-215-B,potr-215-S,potr-219-S,potr-221-S,potr-223-B,potr-225-S,
potr-227-B,potr-229-B,potr-229-S,potr-231-B,potr-233-S,potr-235-B,potr-235-S,potr-237-B,potr-237-S,potr-239-B,
potr-239-S,potr-241-S,potr-243-B,potr-243-S,potr-247-S,potr-251-B,potr-251-S,potr-253-S,potr-257-S,potr-259-B,
potr-261-B,potr-261-S,potr-263-B,potr-263-S,potr-265-B,potr-265-S,potr-267-B,potr-269-S,potr-271-B,potr-273-B,
potr-277-B,potr-277-S,potr-279-B,potr-279-S,potr-281-B,potr-285-B,potr-285-S,potr-287-B,potr-355-L,potr-355-S,
potr-603-B,potr-609-S,potr-611-B,potr-613-S,potr-615-B,potr-615-S,potr-617-S,potr-619-S,potr-621-B,potr-621-S,
potr-637-S,potr-639-B,potr-639-S,potr-641-B,potr-643-B,potr-643-S,potr-645-S,potr-651-B,potr-653-S,potr-655-B,
potr-655-S,potr-657-S,potr-659-B filtered2xHiCov_pando_variants.vcf > pando_friends_4rd.vcf
Then I re-calculate IBD on these individuals only.