User: mahnoornaseer97
mahnoornaseer97 • 0
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Posts by mahnoornaseer97
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Comment:
C: My VCF files are of zero length?
... i have edited my question. there are no error message its just that the vcf files does not have any information after the header? ...
written 9 months ago by
mahnoornaseer97 • 0
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... 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 ...
written 9 months ago by
mahnoornaseer97 • 0
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... IT WORKED!
I WAS USING THE PREVIOUS PATH. i continue with the new one and it worked!Thank you! ...
written 10 months ago by
mahnoornaseer97 • 0
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... 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 months ago by
mahnoornaseer97 • 0
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... 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 months ago by
mahnoornaseer97 • 0
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... 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 10 months ago by
mahnoornaseer97 • 0
• updated
10 months ago by
WouterDeCoster ♦ 28k
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... 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 10 months ago by
mahnoornaseer97 • 0
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... alright ! thanks
But i have tried picards AddOrReplaceReadGroups twice, it still gives the same error? ...
written 10 months ago by
mahnoornaseer97 • 0
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... oh Great!
thank you ...
written 10 months ago by
mahnoornaseer97 • 0
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... `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 ...
written 10 months ago by
mahnoornaseer97 • 0
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