Daniel:Notebook/Haplotyping/2014-1-22
HiC Data Analysis
From the data from Bing Ren's lab, I'm planning on working through the HaploSeq analysis pipeline.
Input Data
The HiC data from Bing Ren's lab can be found on Genome Miner at:
/home/kunzhang/seqStore/140110_HiC_BingRen
Also being used are the hg19 whole genome fasta file:
/GenomeDB/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa
and the PGP1F data, specifically the variant calls from the data from the published paper (Ball et al, PNAS 2005):
PGP1F data
Converting Variant Call File
The variant calls from Ball et al were originally in a .tsv in the format provided by complete genomics. Most programs use a vcf file so I used a converter, found on the Complete Genomics website, to change the file to the more widely used format.
Convert .tsv to .vcf
./masterVar2VCFv41 var-GS00253-DNA_D02_200_37-ASM.tsv genome.fa.bz2 pgp1f_hg19_vcf.vcf
This should have yielded a .vcf file which tells all of the possible variants at an SNP given the reference genome from hg19.
Novoalign
Mask SNPs using the .vcf file
novoutil iupac pgp1f_hg19_vcf.vcf genome.fa