User: vaish01kv

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Posts by vaish01kv

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VCF OTHERINFO Field
... Can someone please explain what are Strand bias (SB), Mate bias(MB), F1R2 & F2R1 number detotes in a VCF file? What are potential information drawn from these data? It would be really helpful if answered along with some article. TIA. ...
f2r1 orientation bias f1r2 written 10 months ago by vaish01kv0
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Difference between FATHMM SCORE & FATHMM_MKL_CODING_SCORE
... I have 4 columns in my annotated VCF "FATHMM_SCORE, FATHMM_PRED, FATHMM_MKL_CODING_SCORE, FATHMM_MKL_CODING_PRED". Can someone please explain what is the difference between these two scores? ...
annovar output written 11 months ago by vaish01kv0 • updated 11 months ago by Kevin Blighe60k
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Comment: C: Annovar result GT field
... Yes, how to infer from this data? ...
written 11 months ago by vaish01kv0
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Comment: C: Annovar result GT field
... Thanks for your reply. Could you please clarify the difference between genotypes 0/1, 0/2, 0/1/2? ...
written 11 months ago by vaish01kv0
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Annovar result GT field
... I annotated my tumor-normal sample using ANNOVAR. The genotype field (GT) was 0/0 for normal and 0/1 for tumor. Can someone please explain, why do i get 0/0 for normal sample? I'm a beginner & still couldn't understand the concept of GT in VCF file. TIA. ...
genotype gt annovar written 11 months ago by vaish01kv0
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Comment: C: ANNOVAR - column description
... GT:AD:AF:F1R2:F2R1:DP:OBC:OBAM:OBAMRC:OBPa:OBParc:OBPsnp:SB:MB 0/1:2,27:0.931:0,16:2,11:29:CAC:.:.:.:1,1,13,14:1,1,14,13 This is the output of annotated vcf of mine using wAnnovar. Can anyone please explain what OBAM, OBAMRC, OBParc, OBPsnp means? ...
written 11 months ago by vaish01kv0
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Comment: C: Annovar and wannovar
... perl convert2annovar.pl -format vcf4 SampleName.vcf > converted.input perl table_annovar.pl converted.input humandb/ -buildver hg38 -out converted_result -remove -protocol refGene,cytoBand,cosmic70,clinvar_20190305,1000g2015aug_all,1000g2015aug_amr,1000g2015aug_afr,1000g2015aug_eas,10 ...
written 11 months ago by vaish01kv0
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FACTERA, Result interpretation
... How to interpret the output of "FACTERA"? I'm finding it difficult to figure out false positives. Also where can i find the ranking ? Which rearrangement has most impact on the disease? ...
fusion structual variation gene rearrangement written 11 months ago by vaish01kv0
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Comment: C: How can I compare the structural variation detecting ability between each differ
... How to interpret the output of "FACTERA"? I'm finding it difficult to figure out false positives. Also where can i find the ranking ? Which rearrangement has most impact on the disease? ...
written 11 months ago by vaish01kv0
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Comment: C: SnpEff: How to match variants with line ID in 1001 Genomes Project?
... http://snpeff.sourceforge.net/SnpEff_manual.html#databases Read through & please let me know if you could figure out. ...
written 12 months ago by vaish01kv0

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