Tabix -P Vcf Error
1
1
Entering edit mode
9.3 years ago
bibb77 ▴ 90

Hello everyone, I'm handling self-made VCF files and I need to bgzip and tabix -p them ibn order to use some vcf-tools perl scripts. When I apply the tabiz command: Tabix -p vcf file1.vcf.gz the following error appears:

[ti_index_core] the file out of order at line 8

I had previous errors because I had an extra withespace at the end of each line which I removed using:

sed -e 's/ $//' file1.vcf

I have to say that the VCF file is all tab separated.

So, there are the first 20 lines of my vcf file:

##fileformat=VCFv4.1
##source=pseq
##FILTER=<ID=PASS,Description="Passed variant FILTERs">
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    45125
1    109440678    1KG_1_109440678    I    D    .    PASS    .    GT    1/1
1    110655430    1KG_1_110655430    I    D    .    PASS    .    GT    1/1
1    113933669    1KG_1_113933669    I    D    .    PASS    .    GT    1/1
1    1158675    1KG_1_1158675    I    D    .    PASS    .    GT    1/1
1    12343587    1KG_1_12343587    I    D    .    PASS    .    GT    1/1
1    12632789    1KG_1_12632789    I    D    .    PASS    .    GT    1/1
1    1323216    1KG_1_1323216    I    D    .    PASS    .    GT    1/1
1    14106394    1KG_1_14106394    D    I    .    PASS    .    GT    1/1
1    150201529    1KG_1_150201529    I    D    .    PASS    .    GT    1/1
1    150938672    1KG_1_150938672    I    D    .    PASS    .    GT    1/1
1    152085296    1KG_1_152085296    I    D    .    PASS    .    GT    1/1
1    153641026    1KG_1_153641026    I    D    .    PASS    .    GT    1/1
1    167097500    1KG_1_167097500    I    D    .    PASS    .    GT    1/1
1    169512078    1KG_1_169512078    I    D    .    PASS    .    GT    1/1
1    170967308    1KG_1_170967308    I    D    .    PASS    .    GT    1/1
1    171079942    1KG_1_171079942    I    D    .    PASS    .    GT    1/1

Hope you can help me

tabix vcf • 8.9k views
ADD COMMENT
3
Entering edit mode
9.3 years ago

your VCF must be sorted on CHROM/POS . It is not.

http://samtools.sourceforge.net/tabix.shtml

" The input data file must be position sorted and compressed by bgzip..."

ADD COMMENT
1
Entering edit mode

Hence the error message: POS in lines 5-8 goes 109440678, 110655430, 113933669, 1158675.

ADD REPLY
0
Entering edit mode

Thank you Pierre, that was the solution, I used vcf-sort and everything went ok!!

ADD REPLY

Login before adding your answer.

Traffic: 1785 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6