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CHIPMIX NA value #36
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Hi, @iagooteroc
I don't have a direct answer to this question. Both sequencing error and alignment error for ONT reads will be very different from short reads(e.g. different configurations of aligner parameters could change its behavior to choose indel over SNP error, and the dominant indel errors are rare in Illumina reads). It could lead to both losses or gain of heterozygosity depending on various conditions. It is recommended to choose markers in regions that are easy for ONT reads to pass through if permitted.
VB2 is implemented under the assumption of the diploid genomes. If you can detect and skip the CN aberration regions, the assumption will still hold. Fan |
Hello again. We are successfully using VerifyBamID and we are very glad with it. Now, I'm wondering why the CHIPMIX values are NA, when it is stated that it is "NA if the external genotype is unavailable". I'm using
--SVDPrefix $(VERIFY_BAM_ID_HOME)/resource/1000g.phase3.10k.b38.vcf.gz.dat
so the external genotype should be available, right?Thank you again for your time. This is an example of our output:
EDIT:
I also have two more questions:
Would you expect FREEMIX value to be higher due to ONT error rate?
How do you think the program will perform with tumours? What is the expected impact of CN aberrations in the statistics?
Thank you.
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