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|11-17-2010, 01:03 AM||#1|
Join Date: Nov 2010
Help finish the pipeline for human whole exome sequencing with paired reads data
The pipeline for human whole exome sequencing with paired reads data
A, Align samples to genome (BWA): get BAM files
1./bowtie -t -y -S hg18 -1 reads_1.fq -2 reads_2.fq reads.sam
2.samtools view -bS reads.sam > reads.bam
3.samtools sort reads.bam reads.sorted.bam
4.samtools index reads.sorted.bam
B,SNP or indel analysis:
Last edited by wanguan2000; 11-17-2010 at 06:26 PM.
|07-31-2013, 10:51 PM||#2|
Join Date: Jun 2013
I dont know whether now you are active in the seqanswers forum. If you are there, kindly help me out.
I am also like your stage at present.
Once you index sortedbam files, what are the downstream analysis steps for SNP or indel calling.
What are the tools required.
Kindly let me know.
|exome sequencing, paired end|