neanderthals VCF file

Question

[khatami.mahshid]

Hi all,

I need VCF file for neanderthals, I already found Bam files for them in UCSC, but i need VCF file to have their SNP variation. i also found denisovian VCF file,but I want VCF file for neanderthals. can anybody help me?

thanks a lot

Answer 1

[Antonio R. Franco]

Having the BAM file, you can generate a VCF file with samtools

samtools mpileup -v -u -f genome.fa your.bam > variants.vcf

[khatami.mahshid]

what is genome.fa file? where can I download it ?

[Antonio R. Franco]

The genoma.fa file is the fasta file used as reference for the mapping to generate the BAM file