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[BaseRecalibrator] NCBI dbSNP incompatibility w/ Ensembl whole genome
First, thank you for your time and help.
ERROR /00-All.vcf contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT] ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, GL000008.2, GL000009.2, GL000194.1, GL000195.1, GL000205.2, GL000208.1, GL000213.1, GL000214.1, GL000216.2, GL000218.1, GL000219.1, GL000220.1, GL000221.1, GL000224.1, GL000225.1, GL000226.1, KN538364.1, KQ031383.1, KN538369.1, JH159136.1, JH159137.1, KQ031387.1, KN538360.1, KN196484.1, KN196476.1, KN196479.1, KN196473.1, KN196487.1, KN196475.1, KQ090016.1, KN538361.1, KN196474.1, KQ090022.1, KN196478.1, KN196480.1, KQ090028.1, KN196483.1, KN196481.1, KN538363.1, KN538362.1, KQ031385.1, KQ031386.1, KQ031388.1, KN538365.1, KN538366.1, KN538367.1, KN538370.1, KN538373.1, KN538371.1, KQ031384.1, KN538372.1, KQ090021.1, KN196482.1, KQ458386.1, KN196472.1, GL383545.1, GL383546.1, KI270824.1, KI270825.1, KQ090020.1, GL383547.1, KN538368.1, KI270826.1, KI270827.1, KI270829.1, KI270830.1, KI270831.1, KI270832.1, KI270902.1, KI270903.1, KI270927.1, GL877875.1, GL383549.1, GL383550.2, KQ090023.1, GL877876.1, GL383552.1, KI270904.1, GL383553.2, KI270835.1, GL383551.1, KI270837.1, KI270833.1, KI270834.1, KI270836.1, KI270838.1, KI270839.1, KI270840.1, KI270841.1, KI270842.1, KI270843.1, KQ090024.1, KQ090025.1, KI270844.1, KI270845.1, KI270846.1, KI270847.1, KI270852.1, KI270848.1, GL383554.1, KI270906.1, GL383555.2, KI270851.1, KI270849.1, KI270905.1, KI270850.1, KQ031389.1, KI270853.1, GL383556.1, GL383557.1, KI270855.1, KQ031390.1, KI270856.1, KQ090027.1, KQ090026.1, KI270854.1, KI270909.1, GL383563.3, KI270861.1, GL383564.2, GL000258.2, KI270860.1, KI270907.1, KI270862.1, ... ... (contracted to meet character limit)
Specifically the genome sequence has 'chr' and (also unplaced contigs) but the SNP vcf file does not. I appended 'chr' using:
sed -e '/^[^#]/s/^/chr/' -e 's/^chrMT/chrM/'
Will it matter if the SNP vcf file does not included all the unplaced contigs that my reference genome has?
Also I saw that Ensembl also has publicly available variant vcf files - one has germline variants and another has somatic variants.
For the purpose of using MuTect2 for my tumor samples, are the somatic variant vcf the same thing as Sanger's COSMIC file?
If not, is it advisable to merge the two variant files into 1 SNP file?
EDIT: I also see that NCBI has a separate SNP file for unplaced contigs (should I merge the two?) and that UCSC has its own SNP (following Ensembl format) for common, clinically-associated, and multimapped variants. With so many options which would be preferable for GATK workflow using Ensembl's GRCh38 and GRCh37?