Problems with finding out indels using Unified Genotyper ? (GATK)
I followed the std protocol of First base reaclibarting the .bam file followed by using the realigned .bam file to call for SNPs and Indels.
It calculates snps but shows an error for Indels -
The command I used is
" java -jar GenomeAnalysisTK.jar -I realigned_sample.hg19.sorted.bam -R hg19.fa -T UnifiedGenotyper -glm INDEL -o indelcalls_110527_s_3_1_fq.hg19.vcf -stand_call_conf 50 -S SILENT ".......
I get an error saying - "SAM/BAM file
SAMFileReader{realigned_sample.fq.hg19.bam} is malformed: Adjacent I/D events in read HWUSI-EAS68R:59:1:16:12673:10747 -- cigar: 4M4I3D34M2043N9M" .....
I looked through different forums for this error and its a common problem that many people face. The solutions are unclear and confusing. Can anyone please suggest me clear solution for this ?
Thanks !
I followed the std protocol of First base reaclibarting the .bam file followed by using the realigned .bam file to call for SNPs and Indels.
It calculates snps but shows an error for Indels -
The command I used is
" java -jar GenomeAnalysisTK.jar -I realigned_sample.hg19.sorted.bam -R hg19.fa -T UnifiedGenotyper -glm INDEL -o indelcalls_110527_s_3_1_fq.hg19.vcf -stand_call_conf 50 -S SILENT ".......
I get an error saying - "SAM/BAM file
SAMFileReader{realigned_sample.fq.hg19.bam} is malformed: Adjacent I/D events in read HWUSI-EAS68R:59:1:16:12673:10747 -- cigar: 4M4I3D34M2043N9M" .....
I looked through different forums for this error and its a common problem that many people face. The solutions are unclear and confusing. Can anyone please suggest me clear solution for this ?
Thanks !
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