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

[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:

[vishnuamaram]

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.