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I tried to use FastaAlternateReferenceMaker to create a fasta file using a variant file (with SNPs and INDELs) and GRCh37 reference genome for Chromosome 22 earlier and now Chromosome 19. I noticed that some variants are not incorporated in the output sequence though the QUAL value is 100 and FILTER value is PASS for the variants. There are no overlapping SNPs or INDELs in these locations. For example, when trying to create the output sequence for CHR 19, it did not include the variant in position 540805 in the attached VCF file. Am I missing something? Appreciate your input. I am not able to upload the VCF file. if it would help, here are a few lines from the VCF file:
19 539279 rs2288956 C T 100 PASS AA=C|||;AC=1;AF=0.500;AFR_AF=0.0915;AMR_AF=0.2493;AN=2;DP=11750;EAS_AF=0.1776;EUR_AF=0.2883;NS=2504;SAS_AF=0.1534;VT=SNP GT 1|0
19 539871 rs17672563 C T 100 PASS AA=C|||;AC=1;AF=0.500;AFR_AF=0.0915;AMR_AF=0.2493;AN=2;DP=15431;EAS_AF=0.1746;EUR_AF=0.2883;NS=2504;SAS_AF=0.1554;VT=SNP GT 1|0
19 540648 rs376850117 GC G 100 PASS AA=ccccc|CCCCCC|CCCCC|insertion;AC=1;AF=0.500;AFR_AF=0.7375;AMR_AF=0.9452;AN=2;DP=10125;EAS_AF=0.9018;EUR_AF=0.9384;NS=2504;SAS_AF=0.8814;VT=INDEL GT 1|0
19 540805 rs578255597 G AC 100 PASS AA=?|-|C|unsure;AC=1;AF=0.500;AFR_AF=0.6657;AMR_AF=0.9438;AN=2;DP=9576;EAS_AF=0.999;EUR_AF=0.9294;NS=2504;SAS_AF=0.9162;VT=INDEL GT 1|0
This is the command that I used:
java -Xmx2g -jar ../GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -R human_g1k_v37.fasta -T FastaAlternateReferenceMaker --variant outputChr19NA07056Edited.vcf -o 1000Genomes_chr19outputNA07056.fasta -L 19