Question: the number of the reads covering the snp after HaplotypeCaller
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543541656 • 20 wrote:
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
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modified 10 weeks ago
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Pierre Lindenbaum ♦ 134k
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written
10 weeks ago by
543541656 • 20
