I had sequencing two exome pools,one with 25 normal persons ,and another with 31 patients,
I see crisp could deal with different pools size
so I create a file bam.txt as follows:
./H/pe_realign_recal.bam PS=50
./I/pe_realign_recal.bam PS=62
my running command is:
CRISP --bams bams.txt --ref ucsc.hg19.fasta --VCF crisp2.vcf --bed S07604514_Regions_V6.bed > variantcalls.log
but I got wrong result ,
poolsizes are variable and read from file: 50...805553272
finished reading bam file indexes
reading chromosome chrM offset 6 # targeted bases on chrom is 0/16571
processing 144 reads left in queue for chrom chrM...cleaning read queue from prev chrom
.....finished processing reads for chrom chrM
reading chromosome chr1 offset 16915 # targeted bases on chrom is 6066056/249250621
.....processed 1000000 reads QSIZE:14 chr1:6544493:6544643 variants called 0
.....processed 2000000 reads QSIZE:807 chr1:16458385:16458535 variants called 0
.....processed 3000000 reads QSIZE:196 chr1:23101464:23101614 variants called 0
.....processed 4000000 reads QSIZE:118 chr1:32670269:32670419 variants called 0
I had sequencing two exome pools,one with 25 normal persons ,and another with 31 patients, I see crisp could deal with different pools size so I create a file bam.txt as follows: ./H/pe_realign_recal.bam PS=50 ./I/pe_realign_recal.bam PS=62 my running command is: CRISP --bams bams.txt --ref ucsc.hg19.fasta --VCF crisp2.vcf --bed S07604514_Regions_V6.bed > variantcalls.log but I got wrong result , poolsizes are variable and read from file: 50...805553272 finished reading bam file indexes reading chromosome chrM offset 6 # targeted bases on chrom is 0/16571 processing 144 reads left in queue for chrom chrM...cleaning read queue from prev chrom .....finished processing reads for chrom chrM reading chromosome chr1 offset 16915 # targeted bases on chrom is 6066056/249250621 .....processed 1000000 reads QSIZE:14 chr1:6544493:6544643 variants called 0 .....processed 2000000 reads QSIZE:807 chr1:16458385:16458535 variants called 0 .....processed 3000000 reads QSIZE:196 chr1:23101464:23101614 variants called 0 .....processed 4000000 reads QSIZE:118 chr1:32670269:32670419 variants called 0
How can I solve this problem?