SNP call by samtools, but ALT is "X" QUAL is "0"

[illuminaGA]

Dear All

I had an issue when I did SNP calling by samtools 1.1 with the following commend " samtools mpileup -f hg18chr.fa -u -v 1.bam 2.bam 3.bam 4.bam 5.bam 6.bam 7.bam 8.bam 9.bam -o output.vcf "

The out put file is vcf format but all the ALTs are <X> and all the QUALs are "0"

How can I trouble shoot? Any help is much appreciated

Here is a sample.

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##samtoolsVersion=1.1+htslib-1.1
##samtoolsCommand=samtools mpileup -f hg18chr.fa.fa -u -v -o mutibamtest.vcf 9098.bam 9101.bam 9103.bam 9105.bam 9107.bam 9100.bam 9102.bam 9104.bam 9106.bam
##reference=file://hg18chr.fa.fa
##contig=<ID=chr22,length=49691432>
##ALT=<ID=X,Description="Represents allele(s) other than observed.">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 9098.bam 9101.bam 9103.bam 9105.bam 9107.bam 9100.bam 9102.bam 9104.bam 9106.bam
chr22 14436326 . T G,<X> 0 . DP=1;I16=0,0,1,0,0,0,29,841,0,0,3,9,0,0,0,0;QS=0,1,0;SGB=-0.0293345;MQ0F=0 PL 0,0,0,0,0,0 0,0,0,0,0,0 0,0,0,0,0,0 0,0,0,0,0,0 0,0,0,0,0,0 0,0,0,0,0,0 0,0,0,0,0,0 4,3,0,4,3,4 0,0,0,0,0,0
chr22 14436327 . G <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,1,1,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436328 . G <X> 0 . DP=1;I16=1,0,0,0,26,676,0,0,3,9,0,0,2,4,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436329 . G <X> 0 . DP=1;I16=1,0,0,0,27,729,0,0,3,9,0,0,3,9,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436330 . G <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,4,16,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436331 . C <X> 0 . DP=1;I16=1,0,0,0,29,841,0,0,3,9,0,0,5,25,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436332 . A <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,6,36,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436333 . G <X> 0 . DP=1;I16=1,0,0,0,29,841,0,0,3,9,0,0,7,49,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436334 . G <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,8,64,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436335 . G <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,9,81,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436336 . C <X> 0 . DP=1;I16=1,0,0,0,27,729,0,0,3,9,0,0,10,100,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436337 . C <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,11,121,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436338 . A <X> 0 . DP=1;I16=1,0,0,0,29,841,0,0,3,9,0,0,12,144,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436339 . A <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,13,169,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436340 . A <X> 0 . DP=1;I16=1,0,0,0,29,841,0,0,3,9,0,0,14,196,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436341 . G <X> 0 . DP=1;I16=1,0,0,0,29,841,0,0,3,9,0,0,15,225,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436342 . G <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,16,256,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436343 . A <X> 0 . DP=1;I16=1,0,0,0,27,729,0,0,3,9,0,0,17,289,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436344 . A <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,17,289,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
chr22 14436345 . G <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,16,256,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0

[dpryan]

The command you're looking for is "bcftools call ...", just give it that file.