diff --git a/envs/mtoolbox.yaml b/envs/mtoolbox.yaml
index c0c1b0f..30f614e 100644
--- a/envs/mtoolbox.yaml
+++ b/envs/mtoolbox.yaml
@@ -3,387 +3,23 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - _libgcc_mutex=0.1
-  - _r-mutex=1.0.0
-  - aioeasywebdav=2.2.0
-  - aiohttp=3.4.4
-  - appdirs=1.4.3
-  - asn1crypto=0.24.0
-  - async-timeout=3.0.1
-  - atomicwrites=1.3.0
-  - attrs=18.2.0
-  - backcall=0.1.0
-  - bamutil=1.0.14
-  - bbmap=38.22
-  - bcftools=1.9
-  - bcrypt=3.1.4
-  - binutils_impl_linux-64=2.31.1
-  - binutils_linux-64=2.31.1
-  - biopython=1.72
-  - blas=1.0
-  - bleach=3.1.0
-  - boto3=1.9.35
-  - botocore=1.12.35
-  - bwidget=1.9.11
-  - bzip2=1.0.6
-  - ca-certificates=2020.6.20
-  - cachetools=2.1.0
-  - cairo=1.14.12
-  - certifi=2020.6.20
-  - cffi=1.11.5
-  - chardet=3.0.4
-  - click=7.1.2
-  - configargparse=0.13.0
-  - cryptography=2.4.1
-  - curl=7.64.0
-  - datrie=0.7.1
-  - decorator=4.3.0
-  - defusedxml=0.6.0
-  - docutils=0.14
-  - dropbox=9.1.0
-  - entrypoints=0.3
-  - expat=2.2.6
-  - fastqc=0.11.8
-  - filechunkio=1.6
-  - font-ttf-dejavu-sans-mono=2.37
-  - fontconfig=2.13.0
-  - freetype=2.9.1
-  - fribidi=1.0.5
-  - ftputil=3.2
-  - gatk-framework=3.6.24
-  - gcc_impl_linux-64=7.3.0
-  - gcc_linux-64=7.3.0
-  - gettext=0.19.8.1
-  - gfortran_impl_linux-64=7.3.0
-  - gfortran_linux-64=7.3.0
-  - gitdb2=2.0.5
-  - gitpython=2.1.11
-  - glib=2.56.2
-  - gmap=2018.07.04
-  - gmp=6.1.2
-  - google-auth=1.2.1
-  - google-auth-httplib2=0.0.3
-  - google-cloud-core=0.24.1
-  - google-cloud-storage=1.1.1
-  - google-resumable-media=0.0.2
-  - googleapis-common-protos=1.5.5
-  - graphite2=1.3.12
-  - graphviz=2.40.1
-  - gsl=2.4
-  - gxx_impl_linux-64=7.3.0
-  - gxx_linux-64=7.3.0
-  - harfbuzz=1.8.8
-  - httplib2=0.12.0
-  - icu=58.2
-  - idna=2.7
-  - idna_ssl=1.1.0
-  - importlib_metadata=0.18
-  - intel-openmp=2019.1
-  - ipykernel=5.1.2
-  - ipython=7.2.0
-  - ipython_genutils=0.2.0
-  - jedi=0.13.2
-  - jinja2=2.10.1
-  - jmespath=0.9.3
-  - jpeg=9b
-  - jsonschema=2.6.0
-  - jupyter_client=5.3.1
-  - jupyter_core=4.5.0
-  - krb5=1.16.3
-  - libblas=3.8.0
-  - libcblas=3.8.0
-  - libcurl=7.64.0
-  - libdeflate=1.0
-  - libedit=3.1.20170329
-  - libffi=3.2.1
-  - libgcc=7.2.0
-  - libgcc-ng=8.2.0
-  - libgfortran-ng=7.3.0
-  - libiconv=1.15
-  - liblapack=3.8.0
-  - libopenblas=0.3.7
-  - libpng=1.6.35
-  - libprotobuf=3.6.1
-  - libsodium=1.0.16
-  - libssh2=1.8.0
-  - libstdcxx-ng=8.2.0
-  - libtiff=4.0.9
-  - libuuid=1.0.3
-  - libxcb=1.13
-  - libxml2=2.9.8
-  - line_profiler=2.1.2
-  - make=4.2.1
-  - markupsafe=1.1.0
-  - memory_profiler=0.55.0
-  - mistune=0.8.4
-  - mkl=2018.0.3
-  - mkl_fft=1.0.6
-  - mkl_random=1.0.1
-  - more-itertools=7.2.0
-  - multidict=4.4.2
-  - muscle=3.8.1551
-  - nbconvert=5.5.0
-  - nbformat=4.4.0
-  - ncurses=6.1
-  - networkx=2.2
-  - notebook=6.0.0
-  - numpy=1.15.4
-  - numpy-base=1.15.4
-  - openblas=0.3.7
-  - openjdk=8.0.152
-  - openssl=1.1.1g
-  - packaging=19.0
-  - pandas=0.23.4
-  - pandoc=2.2.3.2
-  - pandocfilters=1.4.2
-  - pango=1.42.4
-  - paramiko=2.4.2
-  - parso=0.3.1
-  - pcre=8.42
-  - perl=5.26.2
-  - pexpect=4.6.0
-  - picard=2.18.16
-  - pickleshare=0.7.5
-  - pip=18.1
-  - pixman=0.34.0
-  - pluggy=0.12.0
-  - prettytable=0.7.2
-  - prometheus_client=0.7.1
-  - prompt_toolkit=2.0.7
-  - protobuf=3.6.1
-  - psutil=5.4.8
-  - pthread-stubs=0.4
-  - ptyprocess=0.6.0
-  - py=1.8.0
-  - pyasn1=0.4.4
-  - pyasn1-modules=0.0.5
-  - pycparser=2.19
-  - pygments=2.3.1
-  - pygraphviz=1.3.1
-  - pynacl=1.3.0
-  - pyopenssl=18.0.0
-  - pyparsing=2.4.2
-  - pysftp=0.2.9
-  - pysocks=1.6.8
-  - pytest=5.0.1
-  - python=3.6.7
-  - python-dateutil=2.7.5
-  - python-irodsclient=0.7.0
-  - python_abi=3.6
-  - pytz=2018.7
-  - pyvcf=0.6.7
-  - pyyaml=3.13
-  - pyzmq=17.1.2
-  - r-abind=1.4_5
-  - r-assertthat=0.2.0
-  - r-backports=1.1.2
-  - r-base=3.5.1
-  - r-base64enc=0.1_3
-  - r-bh=1.66.0_1
-  - r-bindr=0.1.1
-  - r-bindrcpp=0.2.2
-  - r-bookdown=0.7
-  - r-boot=1.3_20
-  - r-broom=0.5.0
-  - r-callr=2.0.4
-  - r-caret=6.0_80
-  - r-cellranger=1.1.0
-  - r-class=7.3_14
-  - r-classint=0.3_3
-  - r-cli=1.0.0
-  - r-clipr=0.4.1
-  - r-cluster=2.0.7_1
-  - r-codetools=0.2_15
-  - r-colorspace=1.3_2
-  - r-crayon=1.3.4
-  - r-crosstalk=1.0.0
-  - r-curl=3.2
-  - r-cvst=0.2_2
-  - r-data.table=1.11.4
-  - r-dbi=1.0.0
-  - r-dbplyr=1.2.2
-  - r-ddalpha=1.3.4
-  - r-deoptimr=1.0_8
-  - r-dichromat=2.0_0
-  - r-digest=0.6.15
-  - r-dimred=0.1.0
-  - r-dplyr=0.7.6
-  - r-drr=0.0.3
-  - r-dt=0.4
-  - r-e1071=1.7_2
-  - r-essentials=3.5.1
-  - r-evaluate=0.11
-  - r-fansi=0.2.3
-  - r-forcats=0.3.0
-  - r-foreach=1.4.4
-  - r-foreign=0.8_71
-  - r-formatr=1.5
-  - r-funr=0.3.2
-  - r-geometry=0.3_6
-  - r-ggplot2=3.0.0
-  - r-glmnet=2.0_16
-  - r-glue=1.3.0
-  - r-gower=0.1.2
-  - r-gtable=0.2.0
-  - r-haven=1.1.2
-  - r-hexbin=1.27.2
-  - r-highr=0.7
-  - r-hms=0.4.2
-  - r-htmltools=0.3.6
-  - r-htmlwidgets=1.2
-  - r-httpuv=1.4.5.1
-  - r-httr=1.3.1
-  - r-ipred=0.9_6
-  - r-irdisplay=0.5.0
-  - r-irkernel=0.8.12
-  - r-iterators=1.0.10
-  - r-jsonlite=1.5
-  - r-kernlab=0.9_26
-  - r-kernsmooth=2.23_15
-  - r-knitr=1.20
-  - r-labeling=0.3
-  - r-labelled=1.1.0
-  - r-later=0.7.3
-  - r-lattice=0.20_35
-  - r-lava=1.6.2
-  - r-lazyeval=0.2.1
-  - r-lubridate=1.7.4
-  - r-magic=1.5_8
-  - r-magrittr=1.5
-  - r-maps=3.3.0
-  - r-markdown=0.8
-  - r-mass=7.3_50
-  - r-matrix=1.2_14
-  - r-mgcv=1.8_24
-  - r-mime=0.5
-  - r-miniui=0.1.1.1
-  - r-modelmetrics=1.1.0
-  - r-modelr=0.1.2
-  - r-munsell=0.5.0
-  - r-nlme=3.1_137
-  - r-nnet=7.3_12
-  - r-numderiv=2016.8_1.1
-  - r-openssl=1.0.2
-  - r-pbdzmq=0.3_3
-  - r-pillar=1.3.0
-  - r-pkgconfig=2.0.1
-  - r-plogr=0.2.0
-  - r-pls=2.6_0
-  - r-plyr=1.8.4
-  - r-praise=1.0.0
-  - r-prettydoc=0.2.1
-  - r-processx=3.1.0
-  - r-prodlim=2018.04.18
-  - r-promises=1.0.1
-  - r-purrr=0.2.5
-  - r-quantmod=0.4_13
-  - r-questionr=0.7.0
-  - r-r6=2.2.2
-  - r-randomforest=4.6_14
-  - r-rbokeh=0.6.3
-  - r-rcolorbrewer=1.1_2
-  - r-rcpp=0.12.18
-  - r-rcpproll=0.3.0
-  - r-readr=1.1.1
-  - r-readxl=1.1.0
-  - r-recipes=0.1.3
-  - r-recommended=3.5.1
-  - r-rematch=1.0.1
-  - r-repr=0.15.0
-  - r-reprex=0.2.0
-  - r-reshape2=1.4.3
-  - r-reticulate=1.12
-  - r-rlang=0.2.1
-  - r-rmarkdown=1.10
-  - r-rmdformats=0.3.5
-  - r-robustbase=0.93_2
-  - r-rpart=4.1_13
-  - r-rprojroot=1.3_2
-  - r-rstudioapi=0.7
-  - r-rvest=0.3.2
-  - r-scales=0.5.0
-  - r-selectr=0.4_1
-  - r-sfsmisc=1.1_2
-  - r-shiny=1.1.0
-  - r-sourcetools=0.1.7
-  - r-spatial=7.3_11
-  - r-squarem=2017.10_1
-  - r-stringi=1.2.4
-  - r-stringr=1.3.1
-  - r-survival=2.42_6
-  - r-testthat=2.0.0
-  - r-tibble=1.4.2
-  - r-tidyr=0.8.1
-  - r-tidyselect=0.2.4
-  - r-tidyverse=1.2.1
-  - r-timedate=3043.102
-  - r-tinytex=0.6
-  - r-ttr=0.23_3
-  - r-utf8=1.1.4
-  - r-uuid=0.1_2
-  - r-viridislite=0.3.0
-  - r-whisker=0.3_2
-  - r-withr=2.1.2
-  - r-xfun=0.3
-  - r-xml2=1.2.0
-  - r-xtable=1.8_2
-  - r-xts=0.11_0
-  - r-yaml=2.2.0
-  - r-zoo=1.8_3
-  - ratelimiter=1.2.0
-  - readline=7.0
-  - requests=2.20.1
-  - rsa=3.1.4
-  - s3transfer=0.1.13
-  - samtools=1.9
-  - scipy=1.3.1
-  - send2trash=1.5.0
+  - samtools=1.11
+  - numpy=1.19.2
+  - picard=2.23.7
+  - bcftools=1.11
+  - trimmomatic=0.39
+  - biopython=1.78
+  - pip=20.2.3
   - seqtk=1.3
-  - setuptools=40.6.2
-  - six=1.11.0
-  - smmap2=2.0.5
-  - snakemake=5.4.3
-  - snakemake-minimal=5.4.3
-  - sqlalchemy=1.2.16
-  - sqlite=3.25.3
-  - terminado=0.8.2
-  - testpath=0.4.2
-  - tk=8.6.9
-  - tktable=2.10
-  - tornado=6.0.3
-  - traitlets=4.3.2
-  - trimmomatic=0.38
-  - urllib3=1.23
-  - wcwidth=0.1.7
-  - webencodings=0.5.1
-  - wheel=0.32.3
-  - wrapt=1.10.11
-  - xmlrunner=1.7.7
-  - xorg-kbproto=1.0.7
-  - xorg-libice=1.0.10
-  - xorg-libsm=1.2.2
-  - xorg-libx11=1.6.8
-  - xorg-libxau=1.0.9
-  - xorg-libxdmcp=1.1.3
-  - xorg-libxext=1.3.4
-  - xorg-libxrender=0.9.10
-  - xorg-renderproto=0.11.1
-  - xorg-xextproto=7.3.0
-  - xorg-xproto=7.0.31
-  - xz=5.2.4
-  - yaml=0.1.7
-  - yarl=1.2.6
-  - zeromq=4.2.5
-  - zipp=0.5.2
-  - zlib=1.2.11
+  - snakemake=5.26
+  - pyvcf=0.6.7
+  - gmap=2020.10.14
+  - yaml=0.2.5
+  - python=3.6
+  - scipy=1.5.2
+  - bamutil=1.0.14
+  - fastqc=0.11.9
+  - gatk-framework=3.6
+  - pandas=1.1.3
   - pip:
-    - apybiomart==0.5.2
-    - asyncio==3.4.3
-    - cython==0.29.20
-    - dask==2.19.0
     - mtoolnote==0.2.0
-    - pysam==0.16.0.1
-    - scikit-allel==1.2.1
-    - toolz==0.10.0
-    - vcfpy==0.12.2
-
diff --git a/install.sh b/install.sh
old mode 100644
new mode 100755
diff --git a/modules/mtVariantCaller.py b/modules/mtVariantCaller.py
index 8f69da0..1cb796e 100644
--- a/modules/mtVariantCaller.py
+++ b/modules/mtVariantCaller.py
@@ -6,6 +6,7 @@
 """
 
 from collections import OrderedDict
+import sys
 import glob
 import gzip
 import math
@@ -23,6 +24,7 @@
 
 
 def extract_mismatches(seq, qs, len_mism, position_in_read):
+    '''extract mismatches from read sequence using MD flag'''
     start = position_in_read - 1
     end = start + len_mism
     mismatch_seq = seq[start:end]
@@ -32,6 +34,7 @@ def extract_mismatches(seq, qs, len_mism, position_in_read):
 
 
 def check_strand(mate):
+    '''check whether read is forward or reverse'''
     if mate & 16 == 16:
         strand = '-'
     else:
@@ -94,6 +97,9 @@ def parse_sam_row(row):
     for field in row[11:]:
         if field.startswith("MD"):
             md = field.split(':')[2]
+            if '*' in md:
+                sys.stderr.write('SAM field without MD flag or with non-canonical MD flag found. Skip this row\n')
+                md = '0'
     leftmost = row[3]-1
     read_id = row[0]
     seq = list(row[9])
@@ -114,8 +120,8 @@ def parse_sam_row(row):
 
 def read_length_from_cigar(cigar_bases, cigar_nt):
     """
-    Cigar bases: ['S', 'M', 'D', 'M', 'I', 'M']
-    Cigar nt:    [10,  30,   5,  15,  10,  20]
+    Cigar nt: ['S', 'M', 'D', 'M', 'I', 'M']
+    Cigar bases:    [10,  30,   5,  15,  10,  20]
 
     The function will compute the effective read length to discard MD variants
     in softclipped regions and to calculate the distance of a mismatch from
@@ -133,8 +139,8 @@ def parse_mismatches_from_cigar_md(sam_record, minqs=25, tail=5,
     """
     Logic of this function is:
 
-    - MD flag reflect the **mapped portion of the read**  - no soft clipping no
-        insertions (although some mutations in softclipped regions have been
+    - MD flag reflects the **mapped portion of the read**  - no soft clipping no
+        insertions
     - CIGAR flag reflects the absolute reads length - including soft clipping
         and insertions;
     - The script first equals the length of the read to that of the mapped
@@ -150,13 +156,12 @@ def parse_mismatches_from_cigar_md(sam_record, minqs=25, tail=5,
             ins_pos_in_seq += int(cigar_bases[n])
         # cut out from the read sequence and qs the bases representing the ins
         elif cigar_nt[n] == 'I':
-            # original version
-            # ins_len = len(cigar_bases[n])
+        # if insertion found then insert in the read sequence and qs the bases representing the ins
             ins_len = int(cigar_bases[n])
             new_seq = new_seq[:ins_pos_in_seq]+new_seq[(ins_pos_in_seq+ins_len):]
             new_qs = new_qs[:ins_pos_in_seq]+new_qs[(ins_pos_in_seq+ins_len):]
-        # insert in the read sequence and qs the bases representing the ins
-        elif cigar_nt[n] == 'D':
+        elif cigar_nt[n] == 'D': #check this
+        # if deletion found then 
             ins_len = int(cigar_bases[n])
             new_seq = new_seq[:ins_pos_in_seq] + ["I"]*ins_len + new_seq[ins_pos_in_seq:]
             new_qs = new_qs[:ins_pos_in_seq] + ["I"]*ins_len + new_qs[ins_pos_in_seq:]
@@ -212,11 +217,10 @@ def parse_mismatches_from_cigar_md(sam_record, minqs=25, tail=5,
                     all_ref.append(bases_ref[x])
                     all_mism.append(new_seq[t])
                     all_qs.append(ord(new_qs[t])-33)
-        except IndexError:
+        except IndexError: #check this  - shouldn't we raise here a more human readable error?
             pass
     return positions_ref_final, positions_read_final, all_ref, all_mism, all_qs, strand
 
-
 def allele_strand_counter(strand):
     """ Initialize a strand counter instance for mismatch detection. """
     if strand == "+":
@@ -245,15 +249,11 @@ def varnames(i):
     refposleft = int(i[3]) - 1
     mate = int(i[1])
     # check strand
-    # TODO: duplicated, can be replaced by check_mate()
-    if mate & 16 == 16:
-        strand = '-'
-    else:
-        strand = '+'
+    strand = check_strand(mate)
     return CIGAR, readNAME, seq, qs, refposleft, strand
 
 
-# defines global variables for MT-table parsing
+# defines global variables for MT-table parsing #check this - this function might be dismissed at some point if we don't use the mt-table anymore
 def varnames2(b, c, i):
     global Position, Ref, Cov, A, C, G, T, A_f, C_f, G_f, T_f, A_r, C_r, G_r, T_r
     Position = int((i[0]).strip())
@@ -621,7 +621,7 @@ def s_encoding(s):
 def mtvcf_main_analysis(mtable_file=None, coverage_data_file=None, sam_file=None,
                         name2=None, tail=5, Q=25, minrd=5, ref_mt=None,
                         tail_mismatch=5):
-    
+
     coverage_data = parse_coverage_data_file(coverage_data_file)
 
     if sam_file.endswith("gz"):
@@ -642,7 +642,8 @@ def mtvcf_main_analysis(mtable_file=None, coverage_data_file=None, sam_file=None
     Coverage = []
     ref = SeqIO.index(ref_mt, 'fasta')
     ref_seq = ref[list(ref.keys())[0]].seq
-    for n in range(len(coverage_data)):
+    #for n in range(len(coverage_data)):
+    for n in range(len(ref_seq)):
         Coverage.append(coverage_data[n + 1])
         mtDNA.append(ref_seq[n])
     mtDNAseq = "".join(mtDNA)