question regarding input.vcf

[beetlejuice007]

Hi,

I need some help.

Can I use bcftools mpileup for creating vcf file from bam files ? Or do I need to run germline caller like GATK or GATK CNV caller. I have WGS bam files.

Also, my vcf file is getting too large when i use bcftools mpileup. It seems each and every position in mentioned in the vcf file. Is that normal ?

Thanks.

bcftools mpileup --bam-list input_files.txt --no-BAQ \
--fasta-ref Homo_sapiens_hg38.fasta \
--indels-cns -min-MQ 60 --min-BQ 20 --ignore-RG --output outfile.vcf.gz -O z9 --threads 24

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRRXXXX.bam SRRYYYY.bam SRRZZZZZ.bam
1 9991 . N <> 0 . DP=1;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0
1 9992 . N T,<> 0 . DP=4;I16=0,0,0,2,0,0,67,2249,0,0,74,2738,0,0,4,8;QS=0,2,0;VDB=0.02;SGB=-0.448442;MQ0F=0 PL 0,0,0,0,0,0 35,3,0,35,3,35 32,3,0,32,3,32
1 9993 . N C,T,<> 0 . DP=15;I16=0,0,0,11,0,0,346,10986,0,0,383,13571,0,0,12,30;QS=0,2.41071,0.589286,0;VDB=4.62332e-08;SGB=-1.33451;MQ0F=0 PL 109,22,7,94,0,91,109,22,94,109 85,9,0,85,9,85,85,9,85,85 47,22,19,28,0,25,47,22,28,47
1 9994 . N C,T,<> 0 . DP=34;I16=0,0,0,27,0,0,821,25405,0,0,734,23448,0,0,25,67;QS=0,1.63384,1.36616,0;VDB=7.55105e-15;SGB=-0.941943;MQ0F=0.0882353 PL
166,106,76,94,0,79,166,106,94,166 143,80,62,82,0,73,143,80,82,143 45,28,22,22,0,19,45,28,22,45
1 9994 . NNNNNNN NCNNNNNN,NNNNNN 0 . INDEL;IDV=5;IMF=0.277778;DP=34;I16=0,3,0,4,120,4800,160,6400,87,2619,136,4732,6,18,9,27;QS=1,0.894737,0.105263;VDB=0.00835905;SGB=1.88363;RPBZ=2.09871;MQBZ=3.80285;SCBZ=4.1003;MQ0F=0 PL 0,9,67,9,67,67 0,0,0,0,0,0 69,9,0,68,1,65
1 9995 . N T,<> 0 . DP=48;I16=0,0,0,38,0,0,1139,34697,0,0,956,31662,0,0,31,57;QS=0,3,0;VDB=4.95864e-19;SGB=-1.95516;MQ0F=0.166667 PL 144,48,0,144,48,144 109,24,0,109,24,109 119,42,0,119,42,119
1 9996 . N T,<> 0 . DP=80;I16=0,0,0,61,0,0,1928,61450,0,0,1709,58923,0,0,96,264;QS=0,3,0;VDB=1.06359e-42;SGB=-1.98339;MQ0F=0.125 PL 164,63,0,164,63,164 146,39,0,146,39,146 166,81,0,166,81,166

[freeseek]

I am not familiar with BCFtools/mpileup but most likely you would need to use BCFtools/mpileup in combination with BCFtools/call to get something usable by MoChA