namsyvo

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namsyvo
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University of Memphis
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Nam Sy Vo

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  • Thank you @Sheila for your quick answer. I saw this statement in the VCF v4.2 documentation: "AF : allele frequency for each ALT allele in the same order as listed: use this when estimated from primary data, not called genotypes". Could yo…
  • Hi, I have a question about how to interpret information in the dbSNP file that is passed to HaplotypeCaller. Let say I have this line in VCF file: CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 14370 rs6054257 G A 29 PASS…
  • Hi, I have a question about interpreting variant quality. Let say I have 8 reads aligned to position 100 with base phred quality as follow: C (REF bases): 28, 29, 31, 31, 31, 32 (6 bases) G (ALT bases): 33, 38 (2 bases) Mapping quality = 60 for all …
  • Thank you for your previous answer. I have one more question, if I provide GATK a VCF file with the option --alleles (together with setting genotyping_mode to be GENOTYPE_GIVEN_ALLELES), is this information used for the calculation of SNP calls, or …
  • I want to make sure about one problem related to this topic. As I understand from the GATK-UGT document, dbSNP files are not used to verify called SNPs in any way while performing SNP calling with GATK-UGT, is that correct? --dbsnp / -D dbSNP file …