User: human_genomeXXX

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Posts by human_genomeXXX

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Comment: C: Need help to choose 2-3 genome annotation software from the list at https://omi
... for mutation profiling, thx ...
written 4.0 years ago by human_genomeXXX10
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Comment: C: Pilon and BBMap generate VCf file where are chromosome names seem to be absent,
... There are no chromosomes in M tuberculosis like in human, as far as i remember Microbiology medschool course.... However, Mycobacterium tuberculosis has circular chromosomes of about 4,200,000 nucleotides long. Genome size is 4 million base pairs, with 3,959 genes; 40% of these genes have had their ...
written 4.0 years ago by human_genomeXXX10
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Comment: C: Pilon and BBMap generate VCf file where are chromosome names seem to be absent,
... I have .sam and .bam alignments to paired fastqs files, thank you ...
written 4.0 years ago by human_genomeXXX10
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Pilon and BBMap generate VCf file where are chromosome names seem to be absent, how to fix that?
... Pilon and BBMap generate VCf file where are chromosome names seem to be absent, how to fix that? Reference is a standard tub. genome. Aligners are BWA and Snap, BBmap, tried all of them. i s it necessary to use gff3 file somehow? ...
pilon annotation vcf bbmap written 4.0 years ago by human_genomeXXX10
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(Closed) Need help to choose 2-3 genome annotation software from the list at https://omictools.com/genome-annotation-category
... Need help to choose 2-3 genome annotation software from the list at https://omictools.com/genome-annotation-category Input will be a VCF files generated from the Pilon, BBMap, GATK and NextGene. Please do not propose SNPEff and VCFAnnotator. Objects of research --- M.Tuberculosis, E. coli, Staf. ...
vcf annotation gff ngs wgs written 4.0 years ago by human_genomeXXX10
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(Closed) How to download tuberculosis reference using the last version of SNPEff?
... How to download tuberculosis reference using the last version of SNPEff? I have tried java -jar snpEff.jar download -v m_tuberculosis.reference ...
snpeff written 4.0 years ago by human_genomeXXX10
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Comment: C: How to preprocess, normalize, decompose a VCF file before inputting to the SNPEf
... There is a "cant find chromosome error" in SNPEff output see VCF`s headers https://www.biostars.org/p/234735/#234856. What exactly commands can fix that? thank you ...
written 4.0 years ago by human_genomeXXX10
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How to preprocess, normalize, decompose a VCF file before inputting to the SNPEff?
... How to preprocess, normalize, decompose a VCF file before inputting to the SNPEff? Heard, people use -sed and -grep to process VCFs somehow. ...
vcf snpeff written 4.0 years ago by human_genomeXXX10
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Comment: C: How to reduce annotation errors using SNPEff on BBMap`s and Pilon`s VCFs?
... I post the other one, it looks unhealthy --- ##fileformat=VCFv4.2 ##BBMapVersion=36.86 ##ploidy=1 ##rarity=1.00000 ##minallelefraction=0.10000 ##reads=789372 ##pairedReads=789372 ##properlyPairedReads=562846 ##readLengthAvg=90.982 ##properPairRate=0.71303 ...
written 4.0 years ago by human_genomeXXX10
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Comment: C: How to reduce annotation errors using SNPEff on BBMap`s and Pilon`s VCFs?
... ##fileformat=VCFv4.1 ##fileDate=20170202 ##source="Pilon version 1.21 Fri Dec 9 16:44:44 2016 -0500" ##PILON="--genome H37Rv_reference.fa --frags file.sorted.bam --output pilon_output.pilon --vcf" ##reference=file:/home/mat29/Desktop/Ready_Genomics_software/H37Rv_reference.fa ...
written 4.0 years ago by human_genomeXXX10

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