DepthOfCoverage Error: no suitable codec found

Question

[whb]

Hi,

I am trying to find the coverage per sample and per gene using GATK DepthOfCoverage. I have downloaded the refseq file as per gatk suggested. But it gave me this error:

A USER ERROR has occurred: Cannot read file://~/hg38.geneTrack.refSeq because no suitable codecs found

gatk DepthOfCoverage \
-R $ref \
-O $outdrive/{} \
-I $input/{}.recal.bam \
-gene-list $refseq \
-L $interval

head hg38.geneTrack.refSeq

#bin    name    chrom   strand  txStart txEnd   cdsStart    cdsEnd  exonCount   exonStarts  exonEnds    score   name2   cdsStartStat    cdsEndStat  exonFrames
0   NM_000299   chr1    +   201283451   201332993   201283702   201328836   15  201283451,201293941,201313165,201316552,201317571,201318617,201319815,201320266,201321977,201323012,201324427,201324940,201325753,201328761,201330073,  201283904,201294045,201313560,201316697,201317779,201318795,201319878,201320381,201322133,201323189,201324581,201325127,201325838,201328868,201332993,  0   PKP1    cmpl    cmpl    0,1,0,2,0,1,2,2,0,0,0,1,2,0,-1,
0   NM_001276351    chr1    -   67092165    67134970    67093004    67127240    8   67092165,67095234,67096251,67115351,67125751,67127165,67131141,67134929,    67093604,67095421,67096321,67115464,67125909,67127257,67131227,67134970,    0   C1orf141    cmpl    cmpl    0,2,1,2,0,0,-1,-1,
0   NM_001005337    chr1    +   201283505   201332989   201283702   201328836   14  201283505,201293941,201313165,201316552,201317571,201318617,201320266,201321977,201323012,201324427,201324940,201325753,201328761,201330073,    201283904,201294045,201313560,201316697,201317779,201318795,201320381,201322133,201323189,201324581,201325127,201325838,201328868,201332989,    0   PKP1    cmpl    cmpl    0,1,0,2,0,1,2,0,0,0,1,2,0,-1,
0   NM_001276352    chr1    -   67092165    67134970    67093579    67127240    9   67092165,67096251,67103237,67111576,67115351,67125751,67127165,67131141,67134929,   67093604,67096321,67103382,67111644,67115464,67125909,67127257,67131227,67134970,   0   C1orf141    cmpl    cmpl    2,1,0,1,2,0,0,-1,-1,

head bed.interval_list

@HD VN:1.6  SO:coordinate
@SQ SN:chr1 LN:248956422    M5:6aef897c3d6ff0c78aff06ac189178dd UR:file:~/hg38/Homo_sapiens_assembly38.fasta
@SQ SN:chr2 LN:242193529    M5:f98db672eb0993dcfdabafe2a882905c UR:file:~/hg38/Homo_sapiens_assembly38.fasta
@SQ SN:chr3 LN:198295559    M5:76635a41ea913a405ded820447d067b0 UR:file:~/hg38/Homo_sapiens_assembly38.fasta
@SQ SN:chr4 LN:190214555    M5:3210fecf1eb92d5489da4346b3fddc6e UR:file:~/hg38/Homo_sapiens_assembly38.fasta
@SQ SN:chr5 LN:181538259    M5:a811b3dc9fe66af729dc0dddf7fa4f13 UR:file:~/hg38/Homo_sapiens_assembly38.fasta
@SQ SN:chr6 LN:170805979    M5:5691468a67c7e7a7b5f2a3a683792c29 UR:file:~/hg38/Homo_sapiens_assembly38.fasta
@SQ SN:chr7 LN:159345973    M5:cc044cc2256a1141212660fb07b6171e UR:file:~/hg38/Homo_sapiens_assembly38.fasta
@SQ SN:chr8 LN:145138636    M5:c67955b5f7815a9a1edfaa15893d3616 UR:file:~/hg38/Homo_sapiens_assembly38.fasta

Thanks!

Answer 1

[Pierre Lindenbaum]

change the suffix .refSeq to .refseq ( see https://github.com/broadgsa/gatk/blob/41147a655594c2aae6e2cad8462bd1648570b32b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java#L78 )

[whb]

Thank you very much! it solved the problem. Could you suggest a way to filter the refseq file so that it only contains the genes/coordinates in the bed file? because I am getting many 0 coverage genes that are not targeted in the panel.

Thank you again!

[Pierre Lindenbaum]

Could you suggest a way to filter the refseq file ...

this is unrelated to the original question. Validate my answer and ask a new question.