Error Loading Vcf File In Ucsc Genome Browser

Question

[win]

Hi all, I generated a vcf file using samtools and the wanted to load it into UCSC Genome Browser as suggested at this link

http://genome.ucsc.edu/goldenPath/help/vcf.html

However, i get an error stating vcf file does not meet regex or something on that lines.

The header of my vcf file is as follows

##fileformat=VCFv4.1
##samtoolsVersion=0.1.18 (r982:295)
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    sorted.read.bam

Any ideas what might be incorrect.

Thanks in advance.

[brentp]

what commands did you use to create the .vcf.gz and .tbi? what does the .bed file with the track line pointing to the vcf.gz contain?

[win]

for .vcf.gz I used bgzip myfile.vcf and for .tbi I used tabix -p vcf myfile.vcf

Answer 1

[Chris Miller]

Try validating your file with VCFtools first. It should provide informative error messages if your file isn't to spec.

[win]

i ran the VCFValidate script against my VCF and i am getting a whole bunch of errors starting with "Number found where operator expected at Line1.........

I am using the latest version of Samtools,

Any ideas?

[Ashutosh Pandey]

Make sure each header statement is on new line. Sometimes the header gets messed up if you move the file between windows and Mac or perform some grep operations.

[Giovanni M Dall'Olio]

You should better open a new question about that. You will get more answers.

[Chris Miller]

Match your errors up to the VCF spec and see if you can figure out what's wrong: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41