fastq and bam files

Question

[smithjamie1]

How to? Using the following alignment entry from a BAM file reconstruct the equivalent FASTQ entry.

ILLUMINA-EAS45_6:1:1:3:2025:0:1:1 0 chr1 115679594 255 36M * 0 0 AAGCACAGGACTATTCTGTCTCATTTTCCAAATAGA ABCABBBCB@@CBCB?B@B?BA@A?A>=68999:59 XM:i:0 NM:i:0 MD:Z:36

[Pierre Lindenbaum]

homework ?

[smithjamie1]

yes, would be great to get some tips. I am familiar with the fastq and usually get my data in the form of vcfs but that is puzzling.

[GenoMax]

See entries for FASTQ format and SAM format. Should be easily apparent what fields to select from your bam to reconstruct the original read.

Answer 1

[mastal511]

Unless this is homework, where you have to write code yourself to do this, there are existing tools that will do the conversion, such as Picard tools SamToFastq, https://broadinstitute.github.io/picard/command-line-overview.html#SamToFastq.