Unaligning BAM files
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samtools sort -n my_alignment.bam my_alignment_qsorted
bedtools bamtofastq -i my_alignment_qsorted.bam -fq /dev/stdout -fq2 /dev/stdout | bwa mem -p /mnt/data/reference/hs37d5.fa - | samtools view -Sb > realigned.bam
If you want to run the GATK, I recommend:
bedtools bamtofastq -i my_alignment_qsorted.bam -fq /dev/stdout -fq2 /dev/stdout | bwa mem -p -R "@RG\tID:foo\tSM:my_sample" /mnt/data/reference/hs37d5.fa - | samblaster | samtools view -Sb - > realigned.bam
Is bamtofastq from bedtools what you need?
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Saulius Lukauskas
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You want to run your reads through "GATK best practices" to do what?
In the meantime, I have the following program: https://github.com/grenaud/libbam/blob/master/removeTagsMapping.cpp
I am trying to find mutations that are present in diseased tissue versus the patients blood.
so you want to run quality score recall and indel realignment and stuff ? You need mapped reads for this.
I do, but I'm trying to use the Galaxy Project and that won't work with TMAP aligned reads
GATK accepts sorted bam files. So, why you want to unalign to raw reads?
I want to be able to use the same methodology in a previous study on a different type of cancer.
Can you please elaborate in brief?
Basically I want to
For these analysis, you don't need raw read files. you can use bam files that you have got. Sort them, if it is not. used this sorted files for MarkDuplicates and further analysis.
So you don't need to obtain reads from your bam files. If you still want to obtain raw reads use
bedtools bamtofastqconversion tool.You may not get unaligned reads in fastq files that you obtain from bam files.
The best thing to do is to ask the sequencing core to provide you with the original fastq files. Also, beware of the the homopolymer repeat error in the Ion torrent data.