User: a.alnawfal.1992
a.alnawfal.1992 • 90
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Posts by a.alnawfal.1992
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... **He Said:**
Here is the context, I tried to align one of whole genome sequencing (WGS) library to **two different references** using bwa (0.7.17) mem program, **one is hg38 reference genome**, the **other is our own human assembly.** After that, we got two bam file, let's call them hg38.bam and ou ...
written 24 days ago by
a.alnawfal.1992 • 90
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... are you aligned reads from human to reference genome that you generated by your own ?! (Not GRCh38 and Not GRCh37) !! if yes!
why would you do that ?! and how do you suspect to have the same result?! ...
written 25 days ago by
a.alnawfal.1992 • 90
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... which tools are you using ? what is the error exactly ? and can you post the command here ? ...
written 25 days ago by
a.alnawfal.1992 • 90
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... Hi Zeinab,
it dose not matter wither you are using Hisat2, BWA or any other alignment program. the most important question is what you want to achieve ?, second question which organism ? thired question is it DNA or RNA?
for the reference you mentioned i believe it's human!, for me i'm using GRCh3 ...
written 25 days ago by
a.alnawfal.1992 • 90
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... Hi,
it's completely depends on what you want to achieve. For example if you Decided to filter variants that have DP less than 5 , so your result is only for variants that have DP more than 5 in terms of false positive, false negative,..etc..
regarding annotation it's very important for detecting dis ...
written 25 days ago by
a.alnawfal.1992 • 90
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... Not Sure about this error, but i used the below command and it's work.
java -jar /home/bioinformatics/picard.jar AddOrReplaceReadGroups -I FileName.bam -O FileName_WithRG.bam -RGID 4 -LB lib1 -PL ILLUMINA -PU unit1 -SM SampleName -SO coordinate
Yours should be :
"PathToYourPicardsToolsIn ...
written 25 days ago by
a.alnawfal.1992 • 90
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... as far as i know, GIAB provides High_Conf.bed + High_Conf.vcf (Available here ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/), No Fastq files are provided.
but Garvan data is available here (ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_Hi ...
written 5 weeks ago by
a.alnawfal.1992 • 90
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... Hi Yussab,
as you did not replay, so i do not know what are you planning to do exactly.
it seems that you do have your own pipeline which mean you have the final VCF where it's generated from NA12878.
i know these 2 tools to compare you result with GIAB Data set. (I do not know if there is somethin ...
written 8 weeks ago by
a.alnawfal.1992 • 90
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... Hi yussab,
few months ago i were working on the same project, but the NA12878 fastq files is generated in house from our sequencer facility. i followed GATK best practice (bwa mem, picard tools and GATK haplotypecaller) and i use our bed file and VCF file with GIAB VCF and High_Conf.bed. to benchmar ...
written 8 weeks ago by
a.alnawfal.1992 • 90
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Answer:
A: vcf-compare alternative in R
... Hi,
i did not use R to Compare 2 vcf files, but i used RTG-tools and Hap.py for validation purpose where GIAB recommend to use one of these tools and both provide you the result as :
1. TP : the variants in both files
2. FP: the variants found in the Quary (Second) file but not in the true file ...
written 11 weeks ago by
a.alnawfal.1992 • 90
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