We find the haplotypecaller is an excellent SNP caller. But recently we got confused for the indel results. We did the target sequencing (total 6 samples with 3 case vs. 3 control). We followed the best practice suggestion except that the VariantRecalibrator (the snp number was around 600 and seems too little for the recalibration). Haploptypecaller detected correctly a SNP but the neighbor deletion was a little strange. From the samtools tview, there is no clear sign for the deletion. We wonder if it came from the de novo assembly by haplotypecaller and is it creditable? Thanks.
The command line:
java -Xmx4g -jar ~/GenomeAnalysisTK-2.1-9-gb90951c/GenomeAnalysisTK.jar -T HaplotypeCaller -R ucsc.hg19.fasta -I sample1.clean.dedup.recal.bam -I sample2.clean.dedup.recal.bam -I sample3.clean.dedup.recal.bam -I sample4.clean.dedup.recal.bam -I sample5.clean.dedup.recal.bam -I sample6.clean.dedup.recal.bam --dbsnp dbsnp_135.hg19.vcf -L target.interval_list -stand_call_conf 50.0 -stand_emit_conf 10.0 -o samples_new.raw.snps.indels.vcf
haplotypecaller result:
SNP: 19448410 . T G 2126.64 . AC=6;AF=0.500;AN=12;ActiveRegionSize=135;ClippingRankSum=18.283;DP=976;EVENTLENGTH=0;FS=1076.837;MLEAC=6;MLEAF=0.500;MQ=58.70;MQRankSum=-2.107;NVH=3;NumHapAssembly=17;NumHapEval=13;QD=2.18;QDE=0.73;ReadPosRankSum=-17.858;TYPE=SNP; GT:GQ:PL 0/1:99:195,0,2945 0/1:99:936,0,6037 0/1:99:354,0,3059 0/1:99:301,0,4595 0/1:99:187,0,2191 0/1:99:203,0,2617
Indel: 19448411 . GTGGCTCC G 274.85 . AC=3;AF=0.250;AN=12;ActiveRegionSize=135;ClippingRankSum=9.296;DP=1019;EVENTLENGTH=-7;FS=328.629;MLEAC=3;MLEAF=0.250;MQ=58.74;MQRankSum=-0.451;NVH=3;NumHapAssembly=17;NumHapEval=13;QD=0.46;QDE=0.15;ReadPosRankSum=-11.624;TYPE=INDEL; GT:GQ:PL 0/0:99:0,106,14388 0/1:99:200,0,28094 0/0:45:0,45,15261 0/1:50:50,0,22048 0/1:74:74,0,10244 0/0:42:0,42,12913