User: mahnoornaseer97

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Posts by mahnoornaseer97

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My VCF files are of zero length?
... i have sorted bam files , i used these command to generate VCF file but my file only has headers, it does not show any alignment? this is the code that i used > samtools mpileup -u -f /home/mahnoor/--------------/reference.fa /home/mahnoor/Documents/IGV_DATA/Wheat_DATA/REFERENCE.sorte ...
R next-gen alignment written 26 minutes ago by mahnoornaseer970 • updated 15 minutes ago by Pierre Lindenbaum96k
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Comment: C: GATK: SAM file doesn't have any read groups defined in the header.
... IT WORKED! I WAS USING THE PREVIOUS PATH. i continue with the new one and it worked!Thank you! ...
written 10 days ago by mahnoornaseer970
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Comment: C: GATK: SAM file doesn't have any read groups defined in the header.
... 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.rg.bam -o /home/mahnoor/Documents/IGV_DATA/Wheat_DATA/reference.bam ...
written 10 days ago by mahnoornaseer970
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Comment: C: GATK: SAM file doesn't have any read groups defined in the header.
... 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.vc ...
written 10 days ago by mahnoornaseer970
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Comment: C: GATK: SAM file doesn't have any read groups defined in the header.
... i changed the previous command a little, i have used this instead java -jar picard.jar AddOrReplaceReadGroups I=/home/mahnoor/Documents/IGV_DATA/Wheat_DATA/reference.rg.bam O=/home/mahnoor/Documents/IGV_DATA/Wheat_DATA/referenceoutput.rg.bam RGID=4 RGLB=lib1 RGPL=illumina RGPU=unit1 ...
written 11 days ago by mahnoornaseer970 • updated 11 days ago by WouterDeCoster20k
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Comment: C: GATK: SAM file doesn't have any read groups defined in the header.
... The exact command for Picards AddOrReplaceReadGroups which i used: java -jar picard.jar AddOrReplaceReadGroups -I reference.bam -O reference.rg.bam RGID=s_6 RGPL=illumina RGPU=HWUSI-EAS535_0025 RGSM=s_6 i used your command, this is what i got `samtools` view -H /home/mahnoor/Documents/IGV_DATA/Wh ...
written 11 days ago by mahnoornaseer970
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Comment: C: GATK: SAM file doesn't have any read groups defined in the header.
... alright ! thanks But i have tried picards AddOrReplaceReadGroups twice, it still gives the same error? ...
written 11 days ago by mahnoornaseer970
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Comment: C: GATK: SAM file doesn't have any read groups defined in the header.
... oh Great! thank you ...
written 11 days ago by mahnoornaseer970
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GATK: SAM file doesn't have any read groups defined in the header.
... `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 de ...
gatk rna-seq written 11 days ago by mahnoornaseer970

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