Hi,
I am a newbie and have limited perl ability, so anyone with working script/program that offers a solution would be much appreciated. I have exon capture data from population level samples that I would eventually like to run through phylogenetic type software like BEAST etc... I have cleaned up datasets and am trying to generate haplotypes from aligned .bam files.
When I try samtools phase and look at the output, the haplotypes are not actually phased (I tried all sorts of perterbations of the options) so I decided to generate a vcf and then run the data through GATKs HaplotypeCaller or ReadBackedPhasing (or both) but my question is, how can I get the phased vcf output back into the full haplotype (with intervening constant bases)? Something similar to what seqphase step2 does with a .const file and the phased output from PHASE. Even better would be a format similar to the one that samtools phase gives that outputs the original .bam file split by haplotype.
Thanks in advance for any help!!
~C
I am a newbie and have limited perl ability, so anyone with working script/program that offers a solution would be much appreciated. I have exon capture data from population level samples that I would eventually like to run through phylogenetic type software like BEAST etc... I have cleaned up datasets and am trying to generate haplotypes from aligned .bam files.
When I try samtools phase and look at the output, the haplotypes are not actually phased (I tried all sorts of perterbations of the options) so I decided to generate a vcf and then run the data through GATKs HaplotypeCaller or ReadBackedPhasing (or both) but my question is, how can I get the phased vcf output back into the full haplotype (with intervening constant bases)? Something similar to what seqphase step2 does with a .const file and the phased output from PHASE. Even better would be a format similar to the one that samtools phase gives that outputs the original .bam file split by haplotype.
Thanks in advance for any help!!
~C
