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Splitting CRAM files

Hello.
It looks like the CRAM files I have consist of multiple genomes' data. If that's even possible, is there a way to split each file into separate ones so that each will include data from a single genome?

cram-files sequence-alignment
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written by langziv • langziv

I need to do variant calling, and I need to associate variants with their respective genome.

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written by langziv • langziv

most SV callers will accept a BED file / a range to call a specific interval.

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written by Pierre Lindenbaum Pierre Lindenbaum

I noticed the problem after I did the variant calling. I got VCF files with no associations between variants and genomes.

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written by langziv • langziv

If this is related to Getting information on CRAM files from headers inside the files then we don't know that there is actually more than one genome in the files you have.

My suspicion is that you don't have multiple genomes. Examine the read headers and see if you have multiple flowcells/lanes/flowcell serials numbers present.

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written by GenoMax GenoMax

Thanks @genomax.
I'm not sure how to identify flowcells/lanes/flowcell serials numbers in CRAM files. Can you give an example?

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written by langziv • langziv

You will need to examine the reads id's in column 1 of the alignments.

Sequence identifiers are explained in this Wikipedia section.

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written by GenoMax GenoMax

Thanks, but this link explains the structure of FASTA files. I don't have FASTA files. My initial data are in CRAM files.

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written by langziv • langziv

Thanks, but this link explains the structure of FASTA files.

it's not. It's about FASTQ.

read carefully what Genomax said:

You will need to examine the reads id's in column 1 of the alignments.

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written by Pierre Lindenbaum Pierre Lindenbaum

So I need to convert the CRAM files to FASTQ files in order to get that information?

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written by langziv • langziv

Yes. You could do this on the fly.

$ samtools view new.bam | cut -f1 -d$'\t' | cut -f1-4 -d$':' | sort | uniq 
NS500177:19:H2HLYAFXX:1
NS500177:19:H2HLYAFXX:2
NS500177:19:H2HLYAFXX:3
NS500177:19:H2HLYAFXX:4

This is the same FC with 4 lanes.

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written by GenoMax GenoMax

Thanks.
So it means that it's a single genome?

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written by langziv • langziv

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