merging and annotating bcf files for variant calling

Question

[pr.khavari]

Hello

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

Error:

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

[barslmn]

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_PRELOAD line come up all time?

[pr.khavari]

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
4 values and 3 alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfieldse