zdr j
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Activity overview
Latest activity by zdr j-
zdr j commented,
Hi Genevieve, Well, as I explained before there is no roundabout step I am taking, the problem is that ICGC data that I am downloading are originally mapped by ICGC or illumina? to GRCh37 (hg19) a...
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zdr j commented,
maybe could not use a liftover tool (crossmap) and I had to realign my reads to hg38? like revert bam to fastq and then BWA MEM and ...?
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zdr j commented,
Got the same problem, tried different references, did not solve the issue. frustrated at GATK Can any one introduce another software to call somatic mutations (small indels and point mutations) tha...
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zdr j commented,
Hi Genevieve, Thank you for your reply. I still have the problem. I think the problem is the reference hg38 file that I am using which I got from Broadinstitute Google bundle. It looks like it does...
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zdr j commented,
Thank you Genevieve, Picard worked to make the dict file. I used samtools to make the fai file. Now running mutect2, I still get this error which is similar to the error I got before when made dict...
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zdr j commented,
Hi Genevieve, Thank you for your help. This is the command I run and the error I get: java -jar ~/picard-2.25.7/picard.jar CreateSequenceDictionary \ R=~/my_project/Homo_sapiens_assembly38.f...
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zdr j commented,
Hello I have exactly the same problem with hg38 reference genome downloaded from google resources of broad institute. I would be thankful if you let us know whether you found the solution? Best
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zdr j created a post,
Error running mutect2 on SAM files remapped to hg38 (original reads were aligned to hg19).
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used: latest version b) Exact command used: c) Entire error log: Hello, I have a problem in running mutect2 and I would be g...
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zdr j commented,
I downloaded "references_hg38_v0_Homo_sapiens_assembly38.fasta" from google cloud broad institute resources and then used: gatk CreateSequenceDictionary \ -R references_hg38_v0_Homo_sapiens_assemb...
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zdr j commented,
Hello, I used crossmap to realign my reads to hg38. but now again I face this problem: "A USER ERROR has occurred: Unknown file is malformed: Could not read sequence dictionary from given fasta fi...