HI,

I've mapped paired end Illumina reads on a genome and generated, using samtools and bcftools a VCF file containing all SNPs. My commands were, after mapping:

samtools view -q 30 -h -b -S xx.sam > xx_cleaned.bam
samtools sort -m 29G -o xx_sorted.bam xx_cleaned.bam
samtools mpileup -t DP -uvf my_genome.fa xx_sorted.bam > xx.vcf
bcftools call -f GQ -o xx_snps.vcf -O v -V indels -cv xx.vcf

My problem is that some SNP entries in the VCF file do not contain all informations. Here are 2 examples, the first one is complete while the 2nd isn't, with the informations RPB and BQB being missing

> Chr1  705231  .   C   A   225.009 .   DP=89;VDB=0.0291683;SGB=-0.692831;RPB=0.0607088;MQB=1;MQSB=1;BQB=0.059068;MQ0F=0;AF1=0.5;AC1=1;DP4=33,17,3,21;MQ=60;FQ=225.007;PV4=1.53914e-05,0.0742308,1,0.282374 GT:PL:DP:GQ 0/1:255,0,255:74:99

> Chr1  167837  .   A   C   221.999 .   DP=59;VDB=0.149773;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=2;DP4=0,0,24,32;MQ=60;FQ=-195.988  GT:PL:DP:GQ 1/1:255,169,0:56:99

Does anyone know why and when some informations are missing in some of the SNP entries ? Thanks.