bedtools sort by faidx

[cmccabe]

The sort order of my bam file is:

cmccabe@DTV-A5211QLM:~/Desktop/NGS/pool_I_090215$ samtools view -H IonXpress_008_150902_newheader.bam | grep SQ | cut -f 2 | awk '{ sub(/^SN:/, ""); print;}'
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrX
chrY
chrM

So I created a names.txt to do a sortBed in bedtools but it appears that the option I need is not there.

Tool:    bedtools sort (aka sortBed)
Version: v2.25.0
Summary: Sorts a feature file in various and useful ways.

Usage:   bedtools sort [OPTIONS] -i <bed/gff/vcf>

Options: 
	-sizeA			Sort by feature size in ascending order.
	-sizeD			Sort by feature size in descending order.
	-chrThenSizeA		Sort by chrom (asc), then feature size (asc).
	-chrThenSizeD		Sort by chrom (asc), then feature size (desc).
	-chrThenScoreA		Sort by chrom (asc), then score (asc).
	-chrThenScoreD		Sort by chrom (asc), then score (desc).
	-faidx (names.txt)	Sort according to the chromosomes declared in "names.txt"
	-header	Print the header from the A file prior to results.

cmccabe@DTV-A5211QLM:~/Desktop/NGS$ sortBed faidx -i /home/cmccabe/Desktop/NGS/bed/bedtools/xgen_targets.bed > /home/cmccabe/Desktop/NGS/bed/bedtools/xgen_targets_sorted.bed

*****ERROR: Unrecognized parameter: faidx *****

Basically, since the sort order of my bam is in "human ordering" I wanted to sort my bed in the same way. Thank you .

[GenoMax]

Did you try

$ sortBed -faidx -i etc.

[cmccabe]

I tried that and got:

Tool:    bedtools sort (aka sortBed)
Version: v2.25.0
Summary: Sorts a feature file in various and useful ways.

Usage:   bedtools sort [OPTIONS] -i <bed/gff/vcf>

Options: 
	-sizeA			Sort by feature size in ascending order.
	-sizeD			Sort by feature size in descending order.
	-chrThenSizeA		Sort by chrom (asc), then feature size (asc).
	-chrThenSizeD		Sort by chrom (asc), then feature size (desc).
	-chrThenScoreA		Sort by chrom (asc), then score (asc).
	-chrThenScoreD		Sort by chrom (asc), then score (desc).
	-faidx (names.txt)	Sort according to the chromosomes declared in "names.txt"
	-header	Print the header from the A file prior to results.


cmccabe@DTV-A5211QLM:~/Desktop/NGS$ sortBed -faidx -i /home/cmccabe/Desktop/NGS/bed/bedtools/xgen_targets.bed > /home/cmccabe/Desktop/NGS/bed/bedtools/xgen_targets_sorted.bed

*****ERROR: Unrecognized parameter: /home/cmccabe/Desktop/NGS/bed/bedtools/xgen_targets.bed *****

I checked the directory where the bed is located as well:

cmccabe@DTV-A5211QLM:~/Desktop/NGS$ ls /home/cmccabe/Desktop/NGS/bed/bedtools
names.txt  names.txt~  xgen_targets.bed  xgen_targets.bed~

Thank you .

Is there a better way to sort by human ordering for the bed file. I have searched but it appears "lexical" ordering is preferred. Thanks.

[HESmith]

Did you actually read the output, or just copy and paste when it didn't work?

-faidx (names.txt)  Sort according to the chromosomes declared in "names.txt"

You have to specify the sorting file when you issue the command, immediately after the option flag.