Sequence Analysis Software

Question

[Zhshqzyc]

Hello, I just got some huge .bam files. For the data mining and whole genome sequence analysis. Which software is better?

Thanks

[Sean Davis]

Perhaps you can be a bit more specific? What is it that you want to do with your large .bam files? Are you comfortable with using command-line software (I hope so)?

[Zhshqzyc]

Goal: Convert bam file to ped file. To get the genetypo.

Answer 1

[Sean Davis]

See the GATK and samtools websites for some ideas to move forward. You'll also need to read some literature and think about how your specific study design will impact common tools for manipulating BAM files and then calling variants. You might want to come back with a more specific question when you have figured out a path forward.

[Zhshqzyc]

I want to pull out the sequence by given the position.

[Sean Davis]

Have you looked at the samtools package? If so, what does it not do that you would like to do?