Problem to index .vcf file to IGV viewer

Question

[lmmartin]

Hello, I'm trying to detect SNPs and Indels in my RNAseq reads. I have mapped the reads to reference (BAM) and I have used Freebayes to call variants (VCF). I have used IGV viewer to the visualization and here is the problem. I load the genome and bam file without problems but I can't index the .vdf file using IVG. I obtain this error when I run the index option: Your input file has a malformed header: we never saw the required CHROM header line (starting with one#) for de input VCF file. My Freebayes version is 4.1.

Someone can help me??

[Pierre Lindenbaum]

'.vdf' file ? If i'ts a not a '.vdf' but a '.vcf', show us the first lines of the VCF file.

[lmmartin]

Here are the first lines. There are a lot of INFO lines but I have only put some lines:

##fileformat=VCFv4.1
##fileDate=20160304
##source=freeBayes v0.9.20
##reference=/data/luisamm_projects/ref_index_build_v3/ref_index.fasta
##phasing=none
##commandline="freebayes -f /data/luisamm_projects/ref_index_build_v3/ref_index.fasta CANUC_R1.sorted.bam"
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  unknown
Bd1     19308   .       CTTCATATTT      ATGCATTTCA      22.8379 .       AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X1M1X3M1X1M2X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=10;MEANALT=1;MQM=3;MQMR=0;NS=1;NUMALT=1;ODDS=5.07517;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=43;