firat zahid
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Activity overview
Latest activity by firat zahid-
firat zahid commented,
Thank you for your answer Tiffanymy reference.dict file looks like : and mybed.bed file looks likes :
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firat zahid commented,
thank you for your answer. no it is not empty. note: I have used the same bed file while generating bam file in "Gatk BaseRecalibrator" and in the first step of CNV calling "PreprocessIntervals" s...
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firat zahid commented,
My genome reference is "hg19_v0_Homo_sapiens_assembly19" that I downloaded it from bundleand my command is: gatk PreprocessIntervals \ -R hg19_v0_Homo_sapiens_assembly19.fasta \ --...
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firat zahid created a post,
PROBLEM: "A USER ERROR has occurred: Badly formed genome unclippedLoc: Contig chr1 given as location, but this contig isn't present in the Fasta sequence dictionary"
Hello there, Im trying to run "PreprocessIntervals" but I get this error: PROBLEM: "A USER ERROR has occurred: Badly formed genome unclippedLoc: Contig chr1 given as location, but this contig isn't...
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firat zahid created a post,
Problem with Germline CNV CollectReadCounts
Hi there,I have generated my bam file from paired end (germline whole exome) fastq by using :bwa mem -> picard Mark duplicates -> Gatk BaseRecalibrator -> Gatk ApplyBQSR Now Im trying to call CNVs ...