Extract bed regions from CRAM files
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3.8 years ago
MAPK ★ 2.1k

Hi Everyone,

I have several hundreds of cram files. I need to extract some bed regions from these files. Is there a way to extract bed regions from cram without unwrapping them to BAM? My final output should be BAM file for selected regions for each sample.

BAM CRAM • 2.9k views
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3.8 years ago
ATpoint 83k

In general the -L option works for CRAM (according to the manual) same as it does for BAM given you indexed them with samtools index.

samtools view --reference ref.fa -L your.bed -o overlaps.bam your.cram
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3.8 years ago
 samtools view -b --reference ref.fa in.cram | bedtools bamtobed -i stdin
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Hi Pierre, I am starting with CRAM not BAM.

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Hi Peter, I am starting with CRAM not BAM.

fixed

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Added -b to your command to avoid unheadered SAM output :)

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ah yes ! thanks you ! :-)

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How is the solution addressing this requirement?

My final output should be BAM file for selected regions for each sample.

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Not sure why this gives me error, but @ATpoint's answer works great.

 [an@user]$ samtools view -b --reference /home/all_sequences.fa /40/AD/XX^92XX^0319.cram | bedtools bamtobed -i genes_build37.bed-hg38
    [W::sam_read1] Parse error at line 1
    Failed to open BAM file ades_genes_build37.bed-hg38
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