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Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
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how do you get homozygous SNPs? #117

Closed kobejamescurry closed 5 years ago

kobejamescurry commented 5 years ago

Sorry, I'm bombarding you with questions... I'd like to make sure my understanding is correct.

Also, I'm wondering how do you utilised read count information from both homozygous and heterzygous SNPs. From what I understood, other ASCN methods usually take vcf file as input to get a view about heterzygous SNPs. However, homozygous SNPs (same as reference) wouldn't be appeared in vcf file. So, may I ask how do you get homozygous SNPs? Do you just assume that all positions that doesn't contain germline SNPs are homozygous?

kobejamescurry commented 5 years ago

in the article of facets, here said homosnp is important image

here said homosnp deletion is not important image

another famous cnv tool Control-FREEC said homosnp gives no information image

you said "A large proportion will be homozygous in any sample but those loci will provide information on total copy number.", so why other ignor this, they also give total copy number or gives extra allele-specific number, and can you give an example of how you make use of homosnp data

so how should I decide which one is right thanks a lot

kobejamescurry commented 5 years ago

when i use for targeted panel, can you give me some recommended arguments, very much thanks

wes, wgs , targeted panel all use the same parameter to get final outputfile snp-pileup -g -q15 -Q20 -P100 -r25,0 vcffile outputfile normalbam tumorbam.

also, my bam chromosome name has chr, so I need to download the vcf in gatk directory should I seleect vcf from the following four(I test common_all_20180423.vcf.gz ), if so, which one is the best(https://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/GATK/)

thanks a lot image