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prepare file for depth of coverage

Trying to prepare a Rod file for use with GATK depth of coverage. I downloaded a standard hg1g refseq file and I need to remove non-standars contigs other then chr1-22 chrx and y and chrM and sort in karotypic order. Is the below the best way to do so? Thank you :).

cat getRefGene.txt | grep -v chrUn* | grep -v *random | grep -v chrM | grep -v *hap* | sort -k1,1 -V -s > output.txt
depth of coverage
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written by bioguy24 bioguy24

grep can accept multiple search patterns in the regex:

grep -vE 'random|chrM|hap|' getRefGene.txt | sort -k1,1 > (...)

I would not use -V as most tools expect standard rather than natural sort order. Ca you show the content of this getRefGene.txt and expected output?

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written by ATpoint ATpoint

input file (getRefegene.txt)

#bin    name    chrom   strand  txStart txEnd   cdsStart    cdsEnd  exonCount   exonStarts  exonEnds    score   name2   cdsStartStat    cdsEndStat  exonFrames
0   NM_001308203.1  chr1    +   66999251    67216822    67000041    67208778    22  66999251,66999928,67091529,67098752,67105459,67108492,67109226,67136677,67137626,67138963,67142686,67145360,67154830,67155872,67160121,67184976,67194946,67199430,67205017,67206340,67206954,67208755,  66999355,67000051,67091593,67098777,67105516,67108547,67109402,67136702,67137678,67139049,67142779,67145435,67154958,67155999,67160187,67185088,67195102,67199563,67205220,67206405,67207119,67216822,  0   SGIP1   cmpl    cmpl    -1,0,1,2,0,0,1,0,1,2,1,1,1,0,1,1,2,2,0,2,1,1,
0   NM_032291.3 chr1    +   66999638    67216822    67000041    67208778    25  66999638,67091529,67098752,67101626,67105459,67108492,67109226,67126195,67133212,67136677,67137626,67138963,67142686,67145360,67147551,67154830,67155872,67161116,67184976,67194946,67199430,67205017,67206340,67206954,67208755,   67000051,67091593,67098777,67101698,67105516,67108547,67109402,67126207,67133224,67136702,67137678,67139049,67142779,67145435,67148052,67154958,67155999,67161176,67185088,67195102,67199563,67205220,67206405,67207119,67216822,   0   SGIP1   cmpl    cmpl    0,1,2,0,0,0,1,0,0,0,1,2,1,1,1,1,0,1,1,2,2,0,2,1,1,

The expected output I believe would be a column 3 with only chr1-22 x y and m. Thank you :).

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written by bioguy24 bioguy24

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