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A Error About Gatk Samfilereader Malformed

I met some questions when using GATK -UnifiedGenoTyper to call SNPs. The code and Error message like this:

 java -jar /WPS/BP/huboqiang/software/GenomeAnalysisTK-1.6-13-g91f02df/GenomeAnalysisTK.jar -T UnifiedGenotyper -I s_6_HW.sorted.bam -R ../hg19.2.fa -o my.vcf --output_mode EMIT_ALL_SITES

##### ERROR MESSAGE: SAM/BAM file SAMFileReader{/WPS/BP/huboqiang/data/BamResult/headerRG.sorted.bam} is malformed: Read HWUSI-EAS535_0025:6:10:13898:5547#0 is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK.  Please use http://www.broadinstitute.org/gsa/wiki/index.php/ReplaceReadGroups to fix this problem

However, this website has been closed so I do not know how to deal with that problem. The Reads mentioned above is:

HWUSI-EAS535_0025:6:1:15164:14102#0     99      chr1    12096   0       76M     =       12243   223     TAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCATAGG    hhhfhhhhhhfhhghffhhgfhhhhhghhehhhhhghhhhgghhghhhhgahghhhhhhfhhghghhhhfehhQd]    XT:A:R  NM:i:0  SM:i:0  AM:i:0  X0:i:7  X1:i:1  XM:i:0  XO:i:0  XG:i:0 MD:Z:76
HWUSI-EAS535_0025:6:1:15164:14102#0     147     chr1    12243   0       76M     =       12096   -223    GCTCATCTCCTTGGCTGTGATACGTGGCCGGCCCTCGCTCCAGCAGCTGGACCCCTACCTGCCGTCTGCTGCCATC    Qa]aaW^X^\[Rb[_W]dcddb]deaadgggaf_a]da_Wffcc`fdfdf]dfdffefffcdcgfggagggegggg    XT:A:R  NM:i:0  SM:i:0  AM:i:0  X0:i:3  X1:i:5  XM:i:0  XO:i:0  XG:i:0 MD:Z:76

And this is a part of the head of the bam file:

@HD     VN:1.0
@SQ     SN:chr1 LN:249250621
@RG     ID:s_6.bam2     PL:illumina     PU:HWUSI-EAS535_0025    SM:s_6.bam
@PG     ID:bwa  PN:bwa  VN:0.6.1-r104

As it mentioned "Read HWUSI-EAS535_0025:6:10:13898:5547#0 is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK.", I do not know what's wrong with the read group @RG or with the BAM header.

Thanks.

gatk bam
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updated by Biostar Biostar • written by huboqiang • huboqiang

1 answer

Your header seems to be right with @RG. However, I don't see the corresponding ID on the read.

For example: This is a header from a bam file I created.

@HD VN:1.0  GO:none SO:coordinate
@SQ SN:C1   LN:304671
@SQ SN:C2   LN:196989
@SQ SN:C3   LN:459830
@SQ SN:C4   LN:18056
@SQ SN:C5   LN:65502
@RG ID:1    PL:illumina  PU:TopHat  LB:S_6_1    SM:U_xy

And my reads are like this:

HWI-EAS431_0038:2:30:10474:19256#0  16  C1  6999    255 71M87N7M    *   0   0   CACCAAGAATCTAATCAAGTGCGCGATTAAGCATACGGCTATGCATCTGGTCATTGTTGATTCAGTCATCACTTTAAG  ECEDDF?GGFDGGDGGFGFCGEGBGFGFFGGGGDGGGGEGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG  MD:Z:78 RG:Z:1  XG:i:0  NH:i:1  NM:i:0  XM:i:0  XO:i:0  AS:i:-1 XS:A:-

Note the RG:Z:1 column, which you don't have. I think this is the problem. Do you use picard tools to add read groups? Or you just add them to your bam header?

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written by Arun Arun

You could use Picard AddOrReplaceReadGroups as follows:

java -Xmx4g -jar AddOrReplaceReadGroups.jar -I s_6_HW.sorted.bam -O s_6_HW.sorted.rg.bam RGID=s_6 RGPL=illumina RGPU=HWUSI-EAS535_0025 RGSM=s_6
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written by Matt Shirley Matt Shirley

I'm sorry Matt I had a hard time logging in this website these days. Thanks, it really works!

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written by huboqiang • huboqiang

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