enter code here
##### ERROR MESSAGE: SAM/BAM/CRAM file
/home/mahnoor/Documents/IGV_DATA/Wheat_DATA/test_wheat/test_data/Ta63c-A1010005_aligned-20.sorted.bam is malformed.
Please see https://software.broadinstitute.org/gatk/documentation/article?id=1317for more information.
Error details: SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups
##### ERROR ------------------------------------------------------------------------------------------
This is the error message that i received. i have tried AddOrReplaceReadGroups and FixMateInformation and ReplaceSamHeader and ValidateSamFile from which i got an ERROR :Missing_Read_Groups.
i am very new to programming and bioinformatics,
i am using this syntax for HAPLOTYPECALLER:
java -jar /home/mahnoor/Documents/SOFTWARES/GATK_MINE/GenomeAnalysisTK.jar -T HaplotypeCaller -R /home/mahnoor/Documents/IGV_DATA/Wheat_DATA/test_wheat/test_data/reference.fa -I /home/mahnoor/Documents/IGV_DATA/Wheat_DATA/reference.bam -o /home/mahnoor/Documents/IGV_DATA/Wheat_DATA/reference.bam.vcf
as you can see i have given all my files the same name in case the system is not recognizing the file.
Can you please let me know what im doing wrong or what else can i do? any help would be much appreciated.
Thank you.
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oh Great! thank you