SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
Base qualities for Illumina Sequencing fongchun Bioinformatics 6 11-29-2011 12:04 AM
Getting map qualities with samtools mpileup? kweber2 Bioinformatics 10 08-04-2011 12:55 AM
Base qualities during qseq2fastq and export2sam conversion hrajasim Illumina/Solexa 1 05-25-2011 11:20 PM
Converting ABI colorspace qualities into base qualities szilva Bioinformatics 7 04-01-2010 11:38 PM
Bowtie, Color-space reads, and confusing base qualities at variable sites keebs42 Bioinformatics 6 03-13-2010 04:51 PM

Reply
 
Thread Tools
Old 05-13-2011, 05:58 AM   #1
hrajasim
Member
 
Location: DC Metro

Join Date: Aug 2009
Posts: 27
Default SAMTOOLS AND GATK input file (base qualities)

I started off with Illumina qseq format - converted to fastq.
I used the sol2std conversion from Maq and used the fastq to align against reference using BWA.
Used the original qseq files to align against reference using ELAND.
I got the output of BWA in SAM format and ELAND in export (which I converted to SAM using export2sam.pl)
Now, the purpose is to detect SNPs and indels using samtools which expects (or interprets) the base qualities in a particular phred scale (Phred+33 correct?).
Could someone help me sort the out the base quality scales in these file formats and what is the correct way to format the input SAM files before running pileup?
Same question for GATK unified caller - what kind of base qualities should I ensure is in the input SAM files?
If I use a standard converter such as sol2std or export2sam how can I be sure the base qualities are in the correct scale?

Thanks in advance.
hrajasim is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:18 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO