Kun:LabNotes/ExonomeSeq/2012-2-22
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HL114 data analysis[edit]
- These libraries were made by Rui from limited number of human fibroblasts. She then did exome capture on the pooled sequencing libraries:Rui's lab notes.
- Two lanes of SE100bp data were generated for the pool of 29 libraries.
- The FASTQ reads were split based on the barcodes into 29 indexes.
- Rui did the BWA mapping, GATK quality recalibration and local alignment using the script fastq2fixedbam.pl.
- I wrote the script split_bam_file.pl to split the combined bam file into 29 bam files for each library.
- I wrote a second script bam_to_pileup.pl to generate pileup files from bam files and calculate the coverage statistics.
- For multiple pileup files in a group, I used a third script mPileup2sncTable.pl to retrieve variants and combine the variants from multiple libraries into a matrix.
1. Move all pileup files in a group to a directory, such as MM 2. Run the command: ./mPileup2sncTable.pl MM >MM_libraries_snc_matrix.txt &
- High-level chromosomal coverage can be calculated using the script getBlockCoverage.pl, which can be either visualized by IGV/UCSC or further analyzed with MS Excel.
./getBlockCoverage.pl < MM/HL114_73.pileup > HL114_Indx73.bedGraph.txt &