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Questions tagged [phred-scores]

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2 votes
1 answer

Can we test the accuracy of Phred scores shown in FASTQ files

Recently I have ran a human WGS on the BGI DNBSEQ system, and their FASTQ quality scores seem to be quite impressive, where the Phred scores barely deteriorate along the read length when checked on ...
benson23's user avatar
  • 151
1 vote
1 answer

Matches, mismatches and indels

I have a bam-file of reads and reference genome. How can I located matches, mismatches and indels in three different files with Phred score in each data of the files?
Shwarz's user avatar
  • 21
3 votes
1 answer

PL and QUAL values on VCF file?

I want to filter my VCF file to include only the relevant information I need but I have some questions about the results I got. This is what the first 10 lines of my VCF file looks like: ...
rimo's user avatar
  • 494