chr10, chr11, chrM, chrX). However, I found one possible solution by sort -V -k1,1 (this works ...
I've been trying to sort a bed file with bedtools and bedops. Both seem to sort the bed file lexicographically. That means if my input test file is: input ...
I'm getting an error from bedops telling me that my bed files are not properly sorted by the chromosome column. In the documentation examples, ...
Sort order of BAM and BED files are different so cannot use -sorted
GATK wants the BAM file sorted in karyotypic order. My fasta is already in karyotypic order when I index it: $ grep '>' hg19.fa >chr1 >chr2 >chr3 >chr4 >chr5 ...
See the following example.txt file:
Sorts a BED file karyotypically. After sorting, it checks if the input and output files have the same content. - @Tabea-K shared this Cacher ...
ERROR This is because all distributed GATK resources are sorted in karyotypic order,
genome sequence with chromosomes in 'karyotypic' sort order, i.e. chr1, chr2, ...
hide all track name="BED track" description="BED format custom track example" visibility=2