User: J.F.Jiang

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J.F.Jiang690
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Posts by J.F.Jiang

<prev • 237 results • page 1 of 24 • next >
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simulate genotypes for SNPs, considering MAF and LD structure
... Hi all, I want to simulate genotypes of several SNPs for 10,000 samples. A Bernoulli sampling is applied to generate SNP genotypes (0/0, 0/1, 1/1) for random samples. However, this will not consier the LD structure among thse SNPs, which was obtained from 1KG dataset. Is there any tools of Gith ...
maf simulation snp genotype ld written 4 months ago by J.F.Jiang690
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Comment: C: extract region bam
... Thanks, Either seal.sh or cutprimers.sh is spliting the raw sequencing file based on matched primers. However, I still want to begin from bam file. ...
written 5 months ago by J.F.Jiang690
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extract region bam
... Hi all, I want to extract bam of specific amplicon to evaluate the according amplicon performance. I used to use samtools view xx.bam chr:start-end to extract the bam, however, if the two amplicon are totally overlapped, this command will return us the whole reads covering the two region. For exam ...
region bam written 5 months ago by J.F.Jiang690 • updated 5 months ago by h.mon15k
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Comment: C: pairwise calculation of relationship based on selected SNPs with MAF>0.3
... I can definitely use vcftools or directly use PLINK to convert vcf to ped, and then use PLINK to calculate IBD. However, genotypes of the samples were saved into database. If I am calculating the pairwise IBD for new 1000 samples against the database. I need to extract the genotypes from database, ...
written 5 months ago by J.F.Jiang690
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pairwise calculation of relationship based on selected SNPs with MAF>0.3
... Hi all, We are genotyping ~2000 SNP in a Panel using NGS method. We want to build a metrics to calculate the relationship for one sample against all in our database, in order to avoid taking wrong samples that are already existed in our lab. I used to use PLINK to calculate IBD score for GWAS dat ...
relationship snp written 5 months ago by J.F.Jiang690
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Comment: C: GATK HaolotypeCaller takes too much time for variant calling
... Actually I also found such a strange issue, when -nct was applied for WGS or WES data, it significantly decrease the runing time, but not for data sequenced from amplicons. ...
written 6 months ago by J.F.Jiang690
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Comment: C: Fasted method to genotype given SNPs from NGS data
... I did add -L snp.bed as the calling restriction, but the runing time did not decrease a lot even using the snp.vcf as the restriction region. ...
written 6 months ago by J.F.Jiang690
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Fasted method to genotype given SNPs from NGS data
... Hi all, We are focusing on 3000 known SNPs. Instead of genotype these SNPs from array or taqman, we use PCR to enrich these SNPs, and get them sequenced on HiSeq. We found genotype these 3000 SNPs cost lots of time. We split the 3000 SNPs into two categories, 1000 of them were called by GATK Un ...
ngs genotype snp written 6 months ago by J.F.Jiang690
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Comment: C: GATK HaolotypeCaller takes too much time for variant calling
... -nt can be only applied in UnifiedGenotyper. Split bam against reference is a kind of simple methods for distributed computation, as bcbio-ngs did. Any other methods? ...
written 6 months ago by J.F.Jiang690
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GATK HaolotypeCaller takes too much time for variant calling
... Hi all, I am using GATK HaplotypeCaller to genotype ~3000 SNPs from amplicon sequencing data, using --genotyping_mode GENOTYPE_GIVEN_ALLELES --alleles $vcf --output_mode EMIT_ALL_SITES mode. Howver, it take huge time to call these variants, ~20h. And I found that adding -nct option did not work, ...
haplotypecaller gatk long written 6 months ago by J.F.Jiang690 • updated 6 months ago by bluemonster080840

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