bcf to vcf Problem

Question

[Alexander Vowinkel]

I have downloaded the BCF of chrY from 1000G phase3:

4532c8cb3234c04e0070c00593768a90 ALL.chrY.phase3_shapeit2_mvncall_integrated.20130502.genotypes.bcf

The header with hexdump looks like this:

00000000  1f 8b 08 04 00 00 00 00  00 ff 06 00 42 43 02 00  |............BC..|
00000010  36 1d ed 5d 7b 8c 5c 57  79 1f 6f a6 d0 0d a5 c4  |6..]{.\Wy.o.....|
00000020  4e 82 1b 28 ca b0 a9 42  d2 da eb 7b de e7 c4 de  |N..(...B...{....|
00000030  c0 78 bd 5e 4c ec b5 63  6f 0c 51 85 dc f5 ee d8  |.x.^L..co.Q.....|
00000040  1e 98 dd 59 66 c6 4e 1d  01 a5 10 91 d2 07 2d 0f  |...Yf.N.......-.|
00000050  41 79 fc 41 a5 22 da 3f  5a 44 5b 01 6d d5 aa 3c  |Ay.A.".?ZD[.m..<|
00000060  44 05 05 2a a4 50 a1 f2  68 2b 15 2a 50 a1 12 20  |D..*.P..h+.*P.. |
00000070  54 24 44 7b ee 7c bf 7b  e7 cc dd 33 f6 d8 8e 93  |T$D{.|.{...3....|

when I do

bcftools view ALL.chrY.[...].bcf > out.vcf

(I tried with version 0.1.19 and 1.2) I get this:

00000000  23 23 66 69 6c 65 66 6f  72 6d 61 74 3d 56 43 46  |##fileformat=VCF|
00000010  76 34 2e 31 0a 02 02 02  02 02 02 02 02 02 02 02  |v4.1............|
00000020  02 02 02 02 02 02 02 02  02 02 02 02 02 02 02 02  |................|
*
00000330  02 02 02 02 02 02 02 04  04 02 02 02 02 02 02 02  |................|
00000340  04 02 02 02 02 02 02 04  02 02 02 02 02 02 02 02  |................|
00000350  02 02 02 02 02 02 02 02  02 02 02 02 02 02 02 02  |................|
*
00000450  60 00 00 00 d4 04 00 00  17 00 00 00 7e 4e f2 00  |`...........~N..|
00000460  01 00 00 00 3d 32 95 44  0b 00 02 00 d1 04 00 01  |....=2.D........|
00000470  07 17 54 17 43 11 00 11  13 17 54 11 14 11 0b 11  |..T.C.....T.....|
00000480  15 15 99 f7 13 3c 11 17  12 c2 04 11 01 12 a3 12  |.....<..........|
00000490  11 16 12 c2 04 11 1b 15  e0 2d 90 3c 11 1a 15 75  |.........-.<...u|
000004a0  02 9a 3b 11 19 15 27 a0  89 3b 11 18 15 00 00 00  |..;...'..;......|
000004b0  00 11 1c 15 00 00 00 00  11 02 11 02 02 02 02 02  |................|
000004c0  02 02 02 02 02 02 02 02  02 02 02 02 02 02 02 02  |................|

Basically a lot of garbage.

Why? What am I doing wrong?

Answer 1

[alons]

Hi there,

What version of bcftools are you using? I presume you use it for variant calling. In the latest version the manual states that "call" replaced "view". We use "call" like this (works fine for us):

bcftools call -vmO z -o var.vcf.gz var.bcf

We base our workflow/pipeline on http://www.htslib.org/workflow/#mapping_to_variant

[Ram]

call replaced view for variant calling, not format conversion. Your solution makes no sense here.

Answer 2

[Ram]

To provide closure to this thread, I think OP using a hexdump on a VCF file to verify output makes no sense. A simple cat would show them that they're indeed getting a VCF file, and adding the -Ov parameter should make that explicit as well.

alons' "solution" makes no sense as OP is trying to use the view functionality and not the variant calling call functionality of bcftools.