Hello everybody.
I am running bcftools on an mpileup file generated by samtools via the following command (I removed the paths and shortened the filenames for clarity):
I then ran bcftools to identify the variation between the sample and the reference genome:
The resulting output file contains many lines with a <*> in the ALT column. Below is a small piece of the output file:
I assume the <*> means there were no reads aligning to these positions of the genome.
I tried various options such as "-U", "-m 2", "-c 1", but they either generated no output or did not do anything.
What option do I use to prevent bcftools from printing the lines containing <*>?
I am running bcftools on an mpileup file generated by samtools via the following command (I removed the paths and shortened the filenames for clarity):
Code:
samtools mpileup -E -uf hg19.fa accepted_hits.bam > accepted_hits.mpileup
Code:
bcftools view -o file.vcf file.mpileup
Code:
1 10497 . C <*> 0 . DP=6;I16=4,2,0,0,237,9429,0,0,300,15000,0,0,136,3166,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,18,192 1 10498 . G <*> 0 . DP=6;I16=4,2,0,0,233,9117,0,0,300,15000,0,0,138,3240,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,18,190 1 10499 . G <*> 0 . DP=6;I16=4,2,0,0,237,9429,0,0,300,15000,0,0,140,3318,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,18,192 1 10500 . G <*> 0 . DP=6;I16=4,2,0,0,233,9117,0,0,300,15000,0,0,142,3400,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,18,190 1 10501 . T <*> 0 . DP=6;I16=4,2,0,0,218,8232,0,0,300,15000,0,0,144,3486,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,18,180 1 10502 . C <*> 0 . DP=6;I16=4,2,0,0,242,9774,0,0,300,15000,0,0,145,3525,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,18,197 1 10503 . T <*> 0 . DP=6;I16=4,2,0,0,238,9462,0,0,300,15000,0,0,146,3566,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,18,193 1 10504 . G <*> 0 . DP=6;I16=4,2,0,0,238,9462,0,0,300,15000,0,0,147,3609,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,18,193 1 10505 . A <*> 0 . DP=6;I16=4,2,0,0,246,10086,0,0,300,15000,0,0,148,3654,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,18,199 1 10506 . C <*> 0 . DP=6;I16=4,2,0,0,242,9774,0,0,300,15000,0,0,149,3701,0,0;QS=1,0;MQSB=1;MQ0F=0 PL 0,18,197
I tried various options such as "-U", "-m 2", "-c 1", but they either generated no output or did not do anything.
What option do I use to prevent bcftools from printing the lines containing <*>?