User: Chadi Saad

gravatar for Chadi Saad
Chadi Saad60
Reputation:
60
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Trusted
Location:
France
Last seen:
4 days, 13 hours ago
Joined:
3 years, 2 months ago
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c*********@hotmail.com

Posts by Chadi Saad

<prev • 25 results • page 1 of 3 • next >
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Question about deduplication with UMI-tools
... Hello, I deduplicated a BAM file using umitools. Before i had : 98186207 after deduplication, I obtain : 58930293 so the ratio is before/after = 1.6 When I calculate the coverage by BED feature before and after dedup, I obtain a ratio of 6 ! I don't understand this difference betwen the cover ...
umi deduplication sequencing written 7 weeks ago by Chadi Saad60 • updated 7 weeks ago by i.sudbery5.3k
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Bcftools merge sample order
... Does the sample names order in the multisample vcf file respect the input files order ? for exemple: >> `bcftools merge sample1.vcf sample2.vcf sample3.vcf` will always produce --> CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sam ...
vcf dna bcftools multisample htslib written 9 months ago by Chadi Saad60 • updated 9 months ago by paolo002140
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Answer: A: Filter multisample vcf for denovo variant
... use [genmod][1] to annotate your variants with genetic models: [1]: http://moonso.github.io/genmod/commands/annotate-models/ ...
written 9 months ago by Chadi Saad60
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Comment: C: Sub sampling bam files (dilution)
... No, i have to do it with this 2 bam files, because they contains some SNP of interest (actually Im trying to dilute SNPs to evaluate a variant caller performance with low allelic ratio variants and sequencing errors). Maybe an idea to do it, is to use your tool : https://github.com/lindenb/jvarkit/w ...
written 23 months ago by Chadi Saad60
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Comment: C: Sub sampling bam files (dilution)
... I'm trying to simulate low allelic ratio variants, by pooling many bam files coming from multiple samples ...
written 23 months ago by Chadi Saad60
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Comment: C: Sub sampling bam files (dilution)
... If the I have 2 bam files with 30x, it doesn't mean that the 2 bam files have exactly the same depth of coverage of each position. so I can't simply take 10% of reads from bam1 and 90% from bam 2. Its depends from the depth coverage at each position. In the final bam, i want to have 10% bam1 and 90 ...
written 23 months ago by Chadi Saad60
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Sub sampling bam files (dilution)
... Hello, I want to realize an in-silico dilution of a bam file into another one. I have 2 bam file (bam1 , bam2), I want to create a bam file (bam3) with 10% of bam1 and 90% bam2 at each sequenced position. How can I do it ? the samtools view -s commande will take a fraction of a bam file, but since ...
ngs alignment bam written 23 months ago by Chadi Saad60
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Comment: C: realignement around Indels
... thanks, but how can I specify my prefered Indel Positions ? (Imagine I have an homopolymer of 5 A , with insertion of 1 A , and I need the aligner to put it in the middle of the homopolyper...) ...
written 2.1 years ago by Chadi Saad60
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realignement around Indels
... Hello, Is it possible to realign reads and force the aligner to put Indels at a certain position, instead of aligning reads to the left ? I found GATK realigner, but it demand an vcf file, while I have just the positions (without the REF / Alt fields in VCF). ...
alignment written 2.1 years ago by Chadi Saad60
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Comment: C: Count mismatchs/Indel number per position in BAM file ?
... thank you ! but can I do it for all positions without -p option ? ...
written 2.2 years ago by Chadi Saad60

Latest awards to Chadi Saad

Popular Question 9 months ago, created a question with more than 1,000 views. For DNA sequences degeneration
Popular Question 22 months ago, created a question with more than 1,000 views. For Extract parts of reads from BAM file that overlap a specific region of genome
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: BAM/SAM to FASTA conversion
Scholar 2.2 years ago, created an answer that has been accepted. For A: BAM/SAM to FASTA conversion

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