User: reza
reza • 210
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- 2 years, 8 months ago
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Posts by reza
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... when i set -ploidy 100, numbers of identified SNPs increased from 23 to 593 ! without apply of -ploidy on 100, my results (23 SNPs) are correct? ...
written 3 months ago by
reza • 210
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... i performed variant calling in mitochondria using whole genome sequencing data by GATK UnifiedGenotyper. Genotype of some SNPs specially those are in D-loop region is heterozygote (0/1). Is it due to heteroplasmy? ...
written 3 months ago by
reza • 210
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... i did it, i described it in my question ...
written 3 months ago by
reza • 210
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... i have vcf file resulted from standard workflow of variant calling (fastq files mapped to reference genome, post-alignment steps, variant calling by samtools). under study species is Bactrian camel ...
written 3 months ago by
reza • 210
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... do you searched about Control-free? ...
written 3 months ago by
reza • 210
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... thanks Kevin
ANNOVAR can help me i guess. i have reference (fasta) file and gff3 file of under study organism. i read ANNOVAR manual for annotation of vcf file by gff3 file but it puzzled me because all the examples are about a human that has all kind of required data. can you help me to do that? a ...
written 3 months ago by
reza • 210
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... hi
i annotated one vcf file using SNPeff and now some SNPs have several effect instead one effect, for example:
ANN=A|splice_acceptor_variant&splice_donor_variant&intron_variant|HIGH|LOC105079267|gene19881|transcript|rna26374|protein_coding|4/6|c.2134+1C
effect of splice_acceptor_vari ...
written 3 months ago by
reza • 210
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... thanks, your suggested way worked fine. ...
written 7 months ago by
reza • 210
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... thanks Pierre, your program worked but i want variants that have LOF tag (in my file 466 variants from 994779 variants). your program give me a file with 1526324 row! ...
written 7 months ago by
reza • 210
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... hi everyone
i annotated my VCF file using snpEff, now i want gene names for LOF (loss of function) variants. how can i do it? anyone can help me? for example in following variant, name of TRAPPC8 gene must be extracted.
KN271071.1 10335196 . G A 217.0 PASS DP=35;VDB=0.8177;SGB=-0.693136;MQSB=0 ...
written 7 months ago by
reza • 210
• updated
7 months ago by
Pierre Lindenbaum ♦ 118k
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For C: Problems with Trimmomatic PE output files
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