Bedtools: Merging Many Bed Files

Bedtools: Merging Many Bed Files


I am using the algorithm CookHLA for my research. As part of its preparation, I need to feed it a bed file representing at least 100 of my samples.

I have made the bed files for 500 samples using samtools and bedtools in a pipeline:

samtools view -@ CPUs -b --reference $REF_FILE $FILE_NAME.cram chr6:29000000-34000000 | bedtools bamtobed -i stdin > ${FILE_NAME}.bed

I then sorted these bed files with the following:

for FILE in * ;  
    echo $FILE
    FILE_NAME=$(echo $FILE | rev | cut -c5- | rev)
    bedtools sort -i $FILE > $FILE_NAME.sorted.bed

Now I want to merge all these sorted bed files into one. I have read into the mergeBed function and intersect offered by bedtools. When running these, I am unfortunately getting the following error:

Error: Sorted input specified, but the file cat_beds.bed has the following out of order record
chr6    28999852    29000003    A00266:357:HFKFMDSXY:4:1449:1127:5791/1 60

Clearly there is a sequence outside of the bounds I specified through samtools. Anyone have advice?




Read more here: Source link