User: Hatem Elshazly

Reputation:
60
Status:
New User
Location:
Egypt
Twitter:
hatem_elshazly
Last seen:
2 years, 9 months ago
Joined:
5 years, 4 months ago
Email:
h*********@gmail.com

Posts by Hatem Elshazly

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Question about Variant Calling: Whole file VS multiple smaller files
... Thanks for your reply, I updated the post with commands. I split a single sample BAM into 4 BAM files with regions, I made sure manually the 4 chunks contained the reads from the original file. ...
written 3.6 years ago by Hatem Elshazly60
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Question about Variant Calling: Whole file VS multiple smaller files
... Hello Everyone, I wanted to test if the resulting VCF would be the same if I split a BAM file before variant calling against calling variants on the whole BAM as input. I made 2 different runs: The 1st run was using the splitted BAMs as inputs to HaplotypeCaller which will output 4 VCF files for e ...
vcf splitting variants genotyper gatk written 3.6 years ago by Hatem Elshazly60 • updated 3.6 years ago by Carlos Borroto1.8k
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Comment: C: GATK's Apply Recalibration not working
... In my case the recal and tranches files were empty, I was using the wrong files but this is not always the cause of this error so there may be a different reason for this error in your case but from my experience you can start with checking the validity of your input files. ...
written 3.6 years ago by Hatem Elshazly60
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Comment: C: FreeBayes vs GATK's HaplotypeCaller
... Great. Thanks! ...
written 3.7 years ago by Hatem Elshazly60
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Comment: C: FreeBayes vs GATK's HaplotypeCaller
... I've just checked the output of GenotypeGVCFs against Freebayes but this time the VCF of GenotypeGVCFs is 981K where as Freebayes is 4.4M. Is this large gap inherent between them (Freebayes and GenotypeGVCFs) or it will shrink when I tune the options? because I want to know if I can safely replace ...
written 3.7 years ago by Hatem Elshazly60
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FreeBayes vs GATK's HaplotypeCaller
... Hello Everyone, I was trying freebayes on a small bam file and wanted to compare the quality of its output -vcf1- against the quality of the output of gatk halplotypecaller -vcf2- but I found there is a huge difference between both of them, for instance vcf1 was 4.4M and vcf2 was 140M. When I trie ...
vcf gatk quality freebayes variant caller written 3.7 years ago by Hatem Elshazly60 • updated 3.7 years ago by Carlos Borroto1.8k
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Comment: C: bwa mem runs slowly the first time
... Thanks for the reply but Is this file saved in a tmp directory or something? I didn't find neither in the reference directory or the working directory. ...
written 4.4 years ago by Hatem Elshazly60
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bwa mem runs slowly the first time
... Hi there, I'm using bwa mem for alignment but I noticed this behavior which I don't fully understand: I created large aws ec2 instances (60G RAM and 32 cores), installed bwa, downloaded the human reference (=3G), indexed it, the bwa command is very straightforward: bwa mem human_ref.fasta input.f ...
mem alignment ec2 slow bwa written 4.4 years ago by Hatem Elshazly60 • updated 4.4 years ago by dariober10k
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Answer: A: GATK's Apply Recalibration not working
... Ok, Luckily I figured it out. There is nothing wrong with the VCF file, the recal and tranches files were empty, I was mislead by the error message! Thanks everyone. ...
written 5.0 years ago by Hatem Elshazly60
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Comment: C: GATK's Apply Recalibration not working
... I tried doing that and it didn't work. Its very weird, in the log info I get this line: INFO  14:21:11,775 ArgumentTypeDescriptor - Dynamically determined type of fileContents.vcf.gz to be VCF  Then the error occurs.   ...
written 5.0 years ago by Hatem Elshazly60

Latest awards to Hatem Elshazly

Popular Question 3.2 years ago, created a question with more than 1,000 views. For Calculating Mapping Coverage
Popular Question 3.2 years ago, created a question with more than 1,000 views. For FreeBayes vs GATK's HaplotypeCaller
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Calculating Mapping Coverage
Popular Question 3.7 years ago, created a question with more than 1,000 views. For samtools merge error
Popular Question 4.4 years ago, created a question with more than 1,000 views. For GATK's Apply Recalibration not working
Scholar 5.0 years ago, created an answer that has been accepted. For A: GATK's Apply Recalibration not working

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