the number of the reads covering the snp after HaplotypeCaller

Question

[543541656]

when I used the following command:

(base) fyx@huangji-5885H-V5:~/bm4_mw/bsa$ samtools view s_add_rmdup.bam Chr11:28164766-28164766 | wc -l
43

we can see that the position 28164766 having 43 reads,but after running the following command:

gatk  HaplotypeCaller  \
-R rice.fasta \
-I input.bam \
--intervals chr11
-O output.g.vcf.gz \

wo can see the folling vcf file,the raw DP of the snp locating 28164766 is 52 and the filtered DP is 48,both are larger than 43,I want to know that's why???

Chr11   28164766    .   G   A   1132.64 .   AC=1;AF=0.500;AN=2;BaseQRankSum=-1.144;DP=52;ExcessHet=3.0103;FS=1.177;MLEAC=1;MLEAF=0.500;MQ=57.58;MQRankSum=4.345;QD=23.60;ReadPosRankSum=2.939;SOR=0.501 GT:AD:DP:GQ:PL  0/1:16,32:48:99:1140,0,576

Answer 1

[pau.rodriguez.sodupe]

Hello

HaplotypeCaller performs local realignment for variant calling. That results in an altered/corrected bam (different to the input bam) from which determines Allele Depths...

If you want to see the bam used for calling you should use the --bamout ${OUTPUT_BAMOUT} argument. This bam will only contain the reads overlaping positions called in the output vcf (normally a much smaller bam file).

Best,

Pau