Hi All,
I don't see any "0/0" call, the final "*_final_snp.vcf" file has "0/1, 1/1 and 1/2". I also loaded the two sample I run on IGV and saw a few instances. One sample called 0/1 and the second sample called 1/1 when both suppose to be called 0/1, when both samples have C and the ref has T in that locus. Any idea?
java -jar $HOME/bin/exome/GenomeAnalysisTK.jar --version
3.6-0-g89b7209
Line executed for single sample:
java -Djava.io.tmpdir=$TEMP -jar -Xmx100g $HOME/bin/exome/GenomeAnalysisTK.jar -T PrintReads -R ref -I CJM1_realigned_reads_R.bam -BQSR CJM1_recal_data.table -o CJM1_recal_reads.bam -nct 27
java -Djava.io.tmpdir=$TEMP -jar -Xmx100g $HOME/bin/exome/GenomeAnalysisTK.jar -T HaplotypeCaller -R $GENOME -I CJM1_recal_reds.bam -o CJM1_raw_variants_recal.vcf -nct 27
java -Djava.io.tmpdir=$TEMP -jar -Xmx100g $HOME/bin/exome/GenomeAnalysisTK.jar -T SelectVariants -R $GENOME -V CJM1_raw_variats_recal.vcf -selectType SNP -o CJM1_raw_snps_recal.vcf
java -Djava.io.tmpdir=$TEMP -jar -Xmx100g $HOME/bin/exome/GenomeAnalysisTK.jar -T VariantFiltration -R $GENOME -V CJM1_raw_snps_recal.vcf --filterExpression 'QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || SOR > 4.0' --filterName "basic_snp_filter" -o CJM1_filtered_snps_final.vcf
Lines Example:
chr1 265086 . A G 159.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.870;ClippingRankSum=0.000;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=5.71;ReadPosRankSum=0.000;SOR=0.582 GT:AD:DP:GQ:PL 0/1:23,5:28:99:188,0,939
chr1 7620221 . A G 63.28 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.71;QD=21.09;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0
chr10 18622015 . G A,T 570.77 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-1.146;ClippingRankSum=0.000;DP=17;ExcessHet=3.0103;FS=3.274;MLEAC=1,1;MLEAF=0.500,0.500;MQ=61.88;MQRankSum=0.617;QD=33.57;ReadPosRankSum=-1.436;SOR=0.595 GT:AD:DP:GQ:PL 1/2:1,12,4:17:99:599,107,156,441,0,517
Regards,
Dereje