Whole Genome from BAM File

[trigremm]

Hello, Im a new to bioinformatics.

I have a whole genome of human in BAM file ~80 Gb. It is already aligned to B19.
can I get certain chromosome "in correct order" if I view BAM file via samtools and concatenate nucleotide strings ? or is there any other way ?

The Bam file is only file I have to work with .

[dpryan]

You might have luck using vcfutils.pl:

samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq

Alternatively, have a look at FastaAlternateReferenceMaker from GATK, which can probably deal with InDels (I don't think that the samtools->bcftools->vcfutils.pl route does).

[trigremm]

thank you for fast response - i will try it