I need to merge my all bcf (binary of vcf) files for filtering but it gave me this error. Note, because I have 100 samples, I have decided to split them into chromosomes.
bcftools merge -o merged_samples_chr1.bcf --file-list bcf_list_chr1
WARNING: Environment variable LD_PRELOAD already has value , will not forward new value [/usr/local/xalt/xalt/lib64/libxalt_init.so] from parent process environment Incorrect number of FORMAT/GL values at chr001:10929036, cannot merge. The tag is defined as Number=G, but found Afterwards, I have checked and find which samples have this sites incorrect number at chr001:chr001:10929036. chr001 10929036 . N A 2 fail CX=AANNN;AC=2;AN=2 GT:FT:DP:MQ:GQ:QD:GL:MC8:AMQ:CS:CG:CX 1/1:q20:1:59:2:2:-99.999,-0.398027:1,0,0,0,0,0,0,0:37:NA:.:WWAAG
Later, I wanted to remove this site or exclude it to new bcf file for samples which have this sites and save it as new bcf without incorrect number of chr.
bcftools annotate -H -e chr001:10929036 BH7L.Chr1.bcf or
bcftools view -x -e 'chr001:10929036' BH7L.Chr1.bcf which gave me this error:
Failed to open file "chr001:10929036" : Protocol not supported Failed to read from chr001:10929036: Protocol not supported
Actually, I am not sure did I assign the right flag and chr expressions to exclude this incorrect site and view the rest of sites?
Thanks in advance
It's probably not a good idea to just remove the errors. You should focus on fixing the first error. Most likely there might be something wrong with the header, could you post your header? Also, does the
LD_PRELOADline come up all time?