Help finish the pipeline for human whole exome sequencing with paired reads data

wanguan2000 · 11-17-2010, 01:03 AM

The pipeline for human whole exome sequencing with paired reads data

A, Align samples to genome (BWA): get BAM files
bowtie
1./bowtie -t -y -S hg18 -1 reads_1.fq -2 reads_2.fq reads.sam
SAM Tools
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:

vishnuamaram · 07-31-2013, 10:51 PM

Quote:

Originally Posted by wanguan2000

The pipeline for human whole exome sequencing with paired reads data

A, Align samples to genome (BWA): get BAM files
bowtie
1./bowtie -t -y -S hg18 -1 reads_1.fq -2 reads_2.fq reads.sam
SAM Tools
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:

Hey wanguan,

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.

Thank you,
Vishnu.

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11-17-2010, 01:03 AM	#1
wanguan2000 Member Location: shanghai Join Date: Nov 2010 Posts: 24	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 bowtie 1./bowtie -t -y -S hg18 -1 reads_1.fq -2 reads_2.fq reads.sam SAM Tools 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.