User: DoubleD

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DoubleD130
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130
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3 years, 3 months ago
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4 years, 2 months ago
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Posts by DoubleD

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Low transition/transversion ratio: alignment or caller problem?
... This is very helpful, thank you Cyriac.  Using the data found at ftp://ftp.sanger.ac.uk/pub/cancer/AlexandrovEtAl/somatic_mutation_data/Liver/ I got a TsTv of 1.222 for the 850734 SNPs in that project. For my dataset, calculating a TsTv on the germline mutations gives a result of 2.1, denoting muta ...
written 3.3 years ago by DoubleD130
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Comment: C: Low transition/transversion ratio: alignment or caller problem?
... Some followup information after talking with a more experienced user; running the TsTv ratio calculation on the germline calls results in 2.06.  Hopefully this denotes a properly aligned BAM, and the low ratio with somatic calls come from too sensitive calling parameters (too lax of parameters to ca ...
written 3.3 years ago by DoubleD130
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Low transition/transversion ratio: alignment or caller problem?
... Hello, After running Varscan and Mutect on a set of 10 patients (tumor / normal comparison), I have run through a pipeline of false-positive filtering.  When I look at my resulting Ts/Tv ratio (by manual calculation, snpEff summary file, SnpSift tstv calculation or GATK VariantEval), it is quite lo ...
vcf somatic qc whole genome written 3.3 years ago by DoubleD130 • updated 3.3 years ago by Cyriac Kandoth4.6k
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Comment: C: Varscan Copy Number Alterration Caller, Number Of Markers
... I don't know if the markers are supposed to be placed on your gene of copy-number interest, or if you mark a relatively normal area as a sort of normalization. I have been working happily with Varscan2 and have generated the copynumber data for 10 whole genomes, although I have yet to process it fu ...
written 3.9 years ago by DoubleD130
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Comment: C: Zero-Read Depth In Samtools Mpileup Causing Problems In Varscan2 With Somatic Mo
... Thanks for passing it along. I ended up using cat /media/BAM/111_N_T.mpileup | awk '{if($4 >= 6) print $0}' | awk '{if($7 != 0) print $0}' | java -jar ~/Downloads/VarScan.v2.3.6.jar somatic -mpileup 1 as it was giving read errors up to 6 reads and then also even though I used -q 1 with samtools ...
written 3.9 years ago by DoubleD130
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Comment: C: Zero-Read Depth In Samtools Mpileup Causing Problems In Varscan2 With Somatic Mo
... Great suggestion, thank you. I'm not missing anything by filtering these spots, since there are zero reads there. If I filter those lines, then it shows an Exception at lines with 1 read, and filtering those, wtih 2 reads, etc. There's the default option that it won't call a variant below 8 reads ...
written 3.9 years ago by DoubleD130
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Zero-Read Depth In Samtools Mpileup Causing Problems In Varscan2 With Somatic Module
... hello. I searched far and wide for a solution to this problem, and saw a post about it maybe being fixed in VarScan 2.3.6, but I'm hainvg it nonetheless. i have been compiling mpileups for use in Varscan2. I have been having some troubles, I think because my mpileups of normal&tumor have line ...
varscan samtools mpileup mutation somatic written 3.9 years ago by DoubleD130 • updated 3.9 years ago by Biostar ♦♦ 20
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Comment: C: Determining The Source Of An Error In Calcbmr
... Lines 301402 - 301407 GL000223.1 173020 173144 AL603926.1 GL000223.1 179011 180456 AL603926.1 GL000223.1 42779 49127 ZNF84 GL000223.1 57229 57328 ZNF84 GL000223.1 57996 58126 ZNF84 GL000223.1 64595 64796 ZNF84 In the index, the relevant line i ...
written 4.0 years ago by DoubleD130
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Comment: C: Best Reference Sequence For Music And "Bit_Test" Error
... I have seen that the autosomes are the same, and just the scaffolding and unmapped regions at the end of the file differ. However, as I posted in a new post this morning, I keep getting an error ERROR: Bit::Vector::Interval_Fill(): maximum index out of range at /usr/local/share/perl/5.14.2/Genome/ ...
written 4.0 years ago by DoubleD130
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Creating A Roi File For The 1000 Genomes Project Reference Version37
... I am trying to make a comprehensive ROI file for music from the 1000 genomes project, since our BAMs and callers used that reference fasta (the human_g1k_v37.fasta). My question is about making sure that I have the right GTF file defining the exon and CDS sequences such that I can make a ROI file f ...
1000genomes music written 4.0 years ago by DoubleD130 • updated 4.0 years ago by Cyriac Kandoth4.6k

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Supporter 3.5 years ago, voted at least 25 times.

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