Kun:LabNotes/Haplotyping/2011-6-14
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Generate the GM12878 reference haplotypes[edit]
- 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 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[edit]
- The 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 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 pileupVsRefHap.pl
./pileupVsRefHap.pl s_4_Indx1.bowtie.pileup > s_4_Indx1.idioGraph.txt &
- Visualize the parental alleles with Idiographica.
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