Daniel:Notebook/Haplotyping/2014-1-22: Difference between revisions
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and the PGP1F data, specifically the variant calls from the data from the published paper (Ball et al, PNAS 2005): | and the PGP1F data, specifically the variant calls from the data from the published paper (Ball et al, PNAS 2005): | ||
[http://www.personalgenomes.org/data/PGP12.05/ PGP1F data] | [http://www.personalgenomes.org/data/PGP12.05/ 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 [http://www.completegenomics.com/analysis-tools/toolrepository/masterVarformattoVCFformatfileconverter/ 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 > hg19_genome_vcfmasked.fa |
Latest revision as of 19:03, 22 January 2014
HiC Data Analysis[edit]
From the data from Bing Ren's lab, I'm planning on working through the HaploSeq analysis pipeline.
Input Data[edit]
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[edit]
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[edit]
Mask SNPs using the .vcf file
novoutil iupac pgp1f_hg19_vcf.vcf genome.fa > hg19_genome_vcfmasked.fa