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  • coverageBed -g option error

    I am using:

    Code:
    cmccabe@DTV-A5211QLM:~/Desktop/NGS$ coverageBed -d -sorted -g /home/cmccabe/Desktop/NGS/bedtools2-25.0/genomes/human.hg19.genome -a /home/cmccabe/Desktop/NGS/bed/bedtools/xgen_targets_sorted.bed -b /home/cmccabe/Desktop/NGS/pool_I_090215/IonXpress_008_150902_newheader.bam > /home/cmccabe/Desktop/NGS/pool_I_090215/IonXpress_008_150902_output.txt
    [B]Error: Sorted input specified, but the file /home/cmccabe/Desktop/NGS/bed/bedtools/xgen_targets_sorted.bed has the following record with a different sort order than the genomeFile /home/cmccabe/Desktop/NGS/bedtools2-25.0/genomes/human.hg19.genome
    chr20	126045	126343	+	DEFB126:exon.2;DEFB126:exon.3[/B]
    The newheader.bam is sorted like so:

    Code:
    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
    Since the bam file is uses "human ordering, I sorted the bed file in the same way using the -faidx option in bedtools.

    Code:
    cmccabe@DTV-A5211QLM:~/Desktop/NGS/bed/bedtools$ awk '!_[$1]++' | cut -f1 xgen_targets_sorted.bed | uniq
    chr1
    chr2
    chr3
    chr4
    chr5
    chr6
    chr7
    chr8
    chr9
    chr10
    chr11
    chr12
    chr13
    chr14
    chr15
    chr16
    chr17
    chr18
    chr19
    chr20
    chr21
    chr22
    chrX
    chrY
    The output file that results stops after chr19. I guess my question is if there was an error sorting wouldn't all the records be a problem and if I made my own genome file using the coordinates in the bedtools genome file but re-ordered them to match mine, would that work? Or is there another problem I am overlooking? Thank you .

    Edit: I just needed a customized genome file and that solved it. Thank you .
    Last edited by cmccabe; 09-30-2015, 04:23 PM. Reason: solved

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