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Problem with vcf file generated
Hi,
I have generated a vcf file from a bam file and reference sequence using the following command
samtools faidx input.reference.fa
samtools index sortedhg19.bam
samtools mpileup -d 8000 -uf input.reference.fa my.sortedhg19.bam | bcftools view -bvcg -> my.raw.bcf
bcftools view my.raw.bcf | perl vcfutils.pl varFilter -D8000 > my.flt.vcf
But when i validated my VCF file using vcf-validator its giving the following error message
The header tag 'reference' not present. (Not required but highly recommended.)
The header tag 'contig' not present for CHROM=chr1. (Not required but highly recommended.)
INFO field at chr1:10007 .. Could not validate the float [-nan]
Can any one help me to fix the third error message .
Can anyone know how to format the reference sequence.?
I have generated VCF file using ref seq in order of chromosomes 1,11,12...19,2,21,..
and also in order 1,2,3... . But in both cases this error exists
I have generated a vcf file from a bam file and reference sequence using the following command
samtools faidx input.reference.fa
samtools index sortedhg19.bam
samtools mpileup -d 8000 -uf input.reference.fa my.sortedhg19.bam | bcftools view -bvcg -> my.raw.bcf
bcftools view my.raw.bcf | perl vcfutils.pl varFilter -D8000 > my.flt.vcf
But when i validated my VCF file using vcf-validator its giving the following error message
The header tag 'reference' not present. (Not required but highly recommended.)
The header tag 'contig' not present for CHROM=chr1. (Not required but highly recommended.)
INFO field at chr1:10007 .. Could not validate the float [-nan]
Can any one help me to fix the third error message .
Can anyone know how to format the reference sequence.?
I have generated VCF file using ref seq in order of chromosomes 1,11,12...19,2,21,..
and also in order 1,2,3... . But in both cases this error exists