Hi there,
I am following the following workflow:
Sample ID from 1000 Genomes project: HG00096
First, indexing the bam file using samtool index
Second, sorting the bam file using samtools sort eg2.bam eg2.sorted
Third, generating a bcf file using samtools mpileup -uf reference_genome_file eg2.sorted.bam | bcftools view -bvcg - > eg2.raw.bcf
The reference human genome file is the one obtained from 1kGenomes, Human_37_*.fasta
Lastly, converting my bcf file to vcf using bcftools view *.bcf | perl /usr/share/samtools/vcfutils.pl varFilter -D100 > *.vcf
I am interested in knowing genotypes for rs numbered dbSNPs and other variants for which I have HG37 genomic coordinates.
When i follow the above workflow, i am not getting 0/0 genotypes and at the same time some of the genomic locations also do not show up. This is why my first question was if absence of variation should be considered a 0/0 genotype?
Thanks,
Ashwin
I am following the following workflow:
Sample ID from 1000 Genomes project: HG00096
First, indexing the bam file using samtool index
Second, sorting the bam file using samtools sort eg2.bam eg2.sorted
Third, generating a bcf file using samtools mpileup -uf reference_genome_file eg2.sorted.bam | bcftools view -bvcg - > eg2.raw.bcf
The reference human genome file is the one obtained from 1kGenomes, Human_37_*.fasta
Lastly, converting my bcf file to vcf using bcftools view *.bcf | perl /usr/share/samtools/vcfutils.pl varFilter -D100 > *.vcf
I am interested in knowing genotypes for rs numbered dbSNPs and other variants for which I have HG37 genomic coordinates.
When i follow the above workflow, i am not getting 0/0 genotypes and at the same time some of the genomic locations also do not show up. This is why my first question was if absence of variation should be considered a 0/0 genotype?
Thanks,
Ashwin
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