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Illumina-Fastq To Sanger-Fastq Conversion

Hi All,

I have some old sequence files generated by CASAVA 1.7 and 1.8. I believe the are in illumina-fastq format. I want to align them now by bwa and then call variation by GATK. DO I need to convert them into Sanger fastq format for this? Whats is the best way to do this.

Thanks and regards.

illumina
• 9,817 views • link
updated by rtliu rtliu • written by peris peris

BWA has "-I" parameter. This tells BWA that the input is in the Illumina 1.3+ read format (quality equals ASCII-64). I am not sure if your problem can be resolved using this parameter. I assume that the output bam file will have sanger fastq encoding. I may be wrong.

• 182 views • link
written by Ashutosh Pandey Ashutosh Pandey

2 answers

Besides FastQC, one may use DetermineFastqQualityEncoding.pl from Macdonald lab to determines quality value encoding format in a given fastq file.

perl DetermineFastqQualityEncoding.pl Read1.fastq

It is usually safer to convert fastq to sanger-fastq encoding first, seqtk is one of such fast conversion tools: (how to install seqtk)

seqtk seq -Q64 -V  Read1.fastq > Read1.sanger.fastq
• 175 views • link
written by rtliu rtliu

Thanks. It was really helpful.

• 0 views • link
written by peris peris

According to the wiki page Illumina 1.8+ (I assume its talking about CASAVA) will be using sanger format. You could check this by either plotting quality value distribution or using a tool like FastQC. I believe, by default, all aligners expect sanger fastq encoding. There is some software listed on the wiki page to convert encoding formats.

• 125 views • link
written by Ying W Ying W

Thanks for the reply.

• 0 views • link
written by peris peris

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