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Kun:LabNotes/Haplotyping/2011-6-14
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==Generate the GM12878 reference haplotypes== *Download the variant files for GM12878, GM12891(father), GM12892(mother) from Complete Genomics' ftp site: ftp://ftp2.completegenomics.com/Pedigree_1463/ASM_Build36_1.10.0/ GS12878-1100-36-ASM-VAR-files.tar GS12891-1100-36-ASM-VAR-files.tar GS12892-1100-36-ASM-VAR-files.tar In Unix, you can use wget to download files: wget ftp://ftp2.completegenomics.com/Pedigree_1463/ASM_Build36_1.10.0/NA12878/GS12878-1100-36-ASM-VAR-files.tar tar -xvf GS12878-1100-36-ASM-VAR-files.tar tar -xvf GS12891-1100-36-ASM-VAR-files.tar tar -xvf GS12892-1100-36-ASM-VAR-files.tar Find the dbSNPAnnotated files, uncompress them bzip2 -d dbSNPAnnotated-GS12878-1100-36-ASM.tsv.bz2 bzip2 -d dbSNPAnnotated-GS12891-1100-36-ASM.tsv.bz2 bzip2 -d dbSNPAnnotated-GS12892-1100-36-ASM.tsv.bz2 *Run the [[Media:trioVar2hap.txt|trioVar2hap.pl]] script to extract the haplotypes for GM12878 trioVar2hap.pl dbSNPAnnotated-GS12878-1100-36-ASM.tsv dbSNPAnnotated-GS12891-1100-36-ASM.tsv dbSNPAnnotated-GS12892-1100-36-ASM.tsv > GM12878_hap.txt ==Analysis of HL095 data== *The [[Rui:LabNotes/Haplotyping/2011-6-4|experiment]] was performed by Rui. **Dilution of 5-cell lysate to ~1pg per reaction; **Tagmentation; **PCR with barcodes; **Pooled and sequencing in one lane, obtained SE80bp reads. *Call variants from each of the 12 files with [[Media:fastq2variants.txt|fastq2variants.pl]]. nohup fastq2variants.pl s_4_Indx1.txt 80 > s_4_Indx1.log & *Compare the alleles called from each file with the GM12878 reference haplotype using [[Media:pileupVsRefHap.txt|pileupVsRefHap.pl]] ./pileupVsRefHap.pl s_4_Indx1.bowtie.pileup > s_4_Indx1.idioGraph.txt & *Visualize the parental alleles with [http://www.ncrna.org/idiographica Idiographica]. [[Image:370858186TASK04720.png|800px]] [[Image:460858749TASK04721.png|800px]] [[Image:12085989TASK04722.png|800px]] [[Image:180859144TASK04723.png|800px]] [[Image:240859843TASK04724.png|800px]] [[Image:290859775TASK04725.png|800px]] [[Image:350859778TASK04726.png|800px]] [[Image:400859757TASK04727.png|800px]] [[Image:460859626TASK04728.png|800px]] [[Image:530859451TASK04729.png|800px]] [[Image:580859248TASK04730.png|800px]] [[Image:040900426TASK04731.png|800px]]
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